### Re: [Fis] Is information physical? A logical analysis

```Mark -- What Shannon referred to as 'entropy' was 'variety'. 'Information'
per se was achieved by way of a reduction or winnowing of this variety of
possibilities, leaving 'information' to survive.

STAN

On Wed, May 30, 2018 at 10:24 PM, Burgin, Mark
wrote:

> Dear Loet,
> Only one remark. There is no Shannon-type information but there is
> Shannon's measure of information, which is called entropy.
>
> Sincerely,
> Mark
>
>
>
> On 5/23/2018 10:44 PM, Loet Leydesdorff wrote:
>
> Dear Mark, Soren, and colleagues,
>
> The easiest distinction is perhaps Descartes' one between* res cogitans*
>  and* res extensa* as two different realities. Our knowledge in each case
> that things could have been different is not out there in the world as
> something seizable such as piece of wood.
>
> Similarly, uncertainty in the case of a distribution is not seizable, but
> it can be expressed in bits of information (as one measure among others).
> The grandiose step of Shannon was, in my opinion, to enable us to
> operationalize Descartes'* cogitans* and make it amenable to the
> measurement as information.
>
> Shannon-type information is dimensionless. It is provided with meaning by
> a system of reference (e.g., an observer or a discourse). Some of us prefer
> to call only thus-meaningful information real information because it is
> embedded. One can also distinguish it from Shannon-type information as
> Bateson-type information. The latter can be debated as physical.
>
> In the ideal case of an elastic collision of "billard balls", the physical
> entropy (S= kB * H) goes to zero. However, if two particles have a
> distribution of momenta of 3:7 before a head-on collision, this
> distribution will change in the ideal case into 7:3. Consequently, the
> probabilistic entropy is .7 log2 (.7/.3) + .3 log2 (.3/.7) =  .86 – .37 =
> .49 bits of information. One thus can prove that this information is not
> physical.
>
> Best,
> Loet
>
> --
>
> Loet Leydesdorff
>
> Professor emeritus, University of Amsterdam
> Amsterdam School of Communication Research (ASCoR)
>
> l...@leydesdorff.net ; http://www.leydesdorff.net/
> Associate Faculty, SPRU, University of
> Sussex;
>
> Guest Professor Zhejiang Univ. ,
> Hangzhou; Visiting Professor, ISTIC,
> Beijing;
>
> Visiting Fellow, Birkbeck , University of London;
>
>
> -- Original Message --
> From: "Burgin, Mark"
> To: "Søren Brier" ; "Krassimir Markov" ;
> "fis@listas.unizar.es"
> Sent: 5/24/2018 4:23:53 AM
> Subject: Re: [Fis] Is information physical? A logical analysis
>
> Dear Søren,
> You response perfectly supports my analysis. Indeed, for you only the
> Physical World is real. So, information has to by physical if it is real,
> or it cannot be real if it is not physical.
> Acceptance of a more advanced model of the World, which includes other
> realities, as it was demonstrated in my book “Structural Reality,” allows
> understand information as real but not physical.
>
>Sincerely,
>Mark
>
> On 5/17/2018 3:29 AM, Søren Brier wrote:
>
> Dear Mark
>
>
>
> Using ’physical’ this way it just tends to mean ’real’, but that raises
> the problem of how to define real. Is chance real? I Gödel’s theorem or
> mathematics and logic in general (the world of form)? Is subjectivity and
> self-awareness, qualia? I do believe you are a conscious subject with
> feelings, but I cannot feel it, see it, measure it. Is it physical then?? I
> only see what you write and your behavior. And are the meaning of your
> sentences physical? So here we touch phenomenology (the experiential) and
> hermeneutics (meaning and interpretation) and more generally semiotics (the
> meaning of signs in cognition and communication). We have problems
> encompassing these aspects in the natural, the quantitative and the
> technical sciences that makes up the foundation of most conceptions of
> information science.
>
>
>
>   Best
>
>   Søren
>
>
>
> *Fra:* Fis   *På
> vegne af *Krassimir Markov
> *Sendt:* 17. maj 2018 11:33
> *Til:* fis@listas.unizar.es; Burgin, Mark
>
> *Emne:* Re: [Fis] Is information physical? A logical analysis
>
>
>
> Dear Mark and FIS Colleagues,
>
>
>
> First of all. I support the idea of Mark to write a paper and to publish
> it in IJ ITA.
>
> It will be nice to continue our common work this way.
>
>
>
> At the second place, I want to point that till now the discussion on
>
> *Is information physical?*
>
> was more-less chaotic – we had no thesis and antithesis to discuss and to
> come to some conclusions.
>
>
>
> I think now, the Mark’s letter may be used as the needed thesis.
>
>
>
> What about the ant-thesis? Well, I will try to write something below.
>
>
>
>
>
> For me, physical, structural and mental  are one and the same.
>
>
>
> Mental ```

### Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa effect"

```Sung -- regarding:

The reason epigenetics (defined here as the process of inheritance without
imlplicating any changes in the nucleotide sequences of DNA)  was not
mentioned in my previous post is because I was mainly interested in the
bottom-up (from micro to macro) mechanism of genetics, not the top-down
(from macro to micro) mechanism.  It is interesting to note that our brain
seems unable to handle both bottom-up and top-down mechanisms
simultaneously, perhaps it may have something to do with the fact that we
have two brain hemispheres (Yin and Yang) but only one vocal cord (the
Dao).

It is interesting that I early realized the difficulty many folks have with
visualizing at one time both the top-down AND bottom-up aspects of the
compositional hierarchy:
[large scale constraints -> [activity in focus <- [small
scale affordances]]]

Perhaps your suggestion is involved here as well!

STAN

On Sat, Apr 28, 2018 at 5:17 PM, Sungchul Ji
wrote:

> Hi Arthur and  FISers,
>
> Thank you for asking an important question. The reason epigenetics
> (defined here as the process of inheritance without imlplicating any
> changes in the nucleotide sequences of DNA)  was not mentioned in my
> previous post is because I was mainly interested in the bottom-up (from
> micro to macro) mechanism of genetics, not the top-down (from macro to
> micro) mechanism.  It is interesting to note that our brain seems unable to
> handle both bottom-up and top-down mechanisms simultaneously, perhaps it
> may have something to do with the fact that we have two brain hemispheres
> (Yin and Yang) but only one vocal cord (the Dao).
>
> One way to integrate the bottom-up and top-down mechanisms underlying
> genetic phenomenon may be to invoke the principle of vibrational resonance
> -- to view both the micro-scale DNA and  the macro-scale environment of
> organisms as vibrational systems or systems of oscillators that can
> exchange information and energy through the well-known mechanisms of
> resonance (e.g., the resonance between the oscillatory motions of the swing
> and the arms of the mother; both motions must have same
> frequencies. otherwise the child will not swing).  According to the
> Fourier theorem, any oscillatory motions of DNA including very low
> frequencies can be generated by linear combinations of  very fast
> covalent bond vibrations in  DNA and  hence can be coupled to slow
> oscillatory motions of the environment, e.g., musical sounds. If this view
> is correct, music can affect, DIRECTLY (i.e., unmediated by the auditory
> system of the brain), the molecular motions of DNA in every cell in our
> body.  In other words, we can hear music not only through our ears but also
> through our whole body including blood.  Because of the patent  issue, I
> cannot reveal the experimental evidence supporting this claim, but, indue
> course, I hope to share with you the scientific evidence we obtained
> recently.
>
> In conclusion, it may be that  the yin-yang doctrine of the Daoist
> philosophy (or any other equivalent principles) applies here, since
> molecular genetics and epigenetics may constitute  the
> irreconcilable opposites:
>
> "Genetics has two complementary aspects -- molecular genetics and
> epigenetics."
>
> "Molecular genetics and epigenetics are the complementary
> aspects of genetics."
>
> "Genetic phenomena can be accounted for in two irreconcilably opposite
> manner with equal validity -- through the bottom-up (or reductionistic) or
> the top-down  (or holistic) approaches."
>
> The last statement would help avoid many wasteful debates in the field of
> genetics.
>
>  If you have any questions or corrections, please let me know.
>
> Sung
>
>
>
>
>
>
>
>
>
>
>
> --
> *From:* Arthur Wist
> *Sent:* Friday, April 27, 2018 6:48 PM
> *To:* Sungchul Ji; FIS FIS
> *Cc:* sbur...@proteomics.rutgers.edu; Sergey Petoukhov;
> ole2001@med.cornell; dani...@shirasawa-acl.net; Sungchul Ji;
> x...@chemistry.harvard.edu; n...@princeton.edu
> *Subject:* Re: [Fis] Fw: The 'Shirasawa phenomenon' or the 'Shirasawa
> effect"
>
> Hi,
>
> Just a short note to first of all say thank you, I've find this very
> helpful to know albeit I can't point to a direct application. Secondly
> however, I do wonder: Why & how come you neglected to - in either an
> inclusionary or exclusionary manner - address any potential epigenetic
> mechanisms?
>
> Kind regards,
>
>
> Arthur
>
> On 20 April 2018 at 19:32, Sungchul Ji  wrote:
> > Hi,
> >
> >
> > I am forwarding a slightly modified version of my previous post with the
> > same title which was rejected by the FIS list due to the heavy
> attachments.
> > The most significant addition is written in green.  The removed
> attachments
> > free of charge.
> >
> >
> > Best.
> >
> >
> > Sung
> >
> > ```

### Re: [Fis] Music : Noise = Meaning : Data

```Bruno -- That is an interesting, creative move!  But my point was simply
that the observer cannot be 'objective', but always
brings in many constraints to any observation, which might have been made
from yet another perspective, of which we cannot
imagine the number or qualities of.

STAN

On Thu, Mar 22, 2018 at 11:41 AM, Bruno Marchal <marc...@ulb.ac.be> wrote:

>
> Dear Stan,
>
>
> On 20 Mar 2018, at 20:22, Stanley N Salthe <ssal...@binghamton.edu> wrote:
>
> Bruno -- In this context I like to point out the constraints on our
> abilities of perception.  First, we are physical.
>
>
> That is a strong metaphysical assumption. See my paper for showing this is
> not compatible with the Digital Mechanist hypothesis in the cognitive
> science, which is my working hypothesis.
>
> Perception is a relative indexical relation between a (digital) machine
> (number, combinators, pattern of game of life, whatever) and other
> plausible, from its perspective, universal or not entities (infinitely many
> below the substitution level, making both matter and consciousness not
> Turing emulable (in the Mechanist perspective).
>
> There are evidences for a physical reality, but I am not sure there are
> evidence for a primary physical reality. The use of math in physics is well
> explained if the physical appears to be a mathematical reality seen from
> internal creature represented, relatively incarnated or implemented in that
> mathematical reality.
>
> I can prove, if you agree with very elementary arithmetic, the existence
> of the computations and the machine running them. I cannot prove the
> existence of a physical universe, but if Mechanism is true, the physical
> universe appearance can and must be explained by a statistics on all
> computations (seen in a first person way). That makes mechanism testable
> and indeed, thanks to Quantum Mechanics (without collapse) it fits very
> well up to now.
>
>
>
>
>
> Thus:
>
> {physical {material {biological {animal {mammal {primate {human
> {socialized {with accumulated personal history }
>
>
>
> Ok, but you will need “magical” (non Turing emulable, nor Recoverable)
> ability in your matter to select some computation.
>
> You invoke the God “Matter", but if it plays a role, I am no more sure I
> can say yes to …the doctor and survive qua computation.
>
> Mechanism and Materialism, which are often used together, can be shown
> incompatible (it is basically my PhD thesis, and it is summed up in most of
> my papers).
>
> So it is more like
>
> {arithmetical{dream-like{biological{conscious{physical{{animal {mammal
> {primate {human {socialized {with accumulated personal history }
>
>
>
>
> Hence, actuality is for us non-existent.
>
>
> ?
> Is not actuality existent *for us*, phenomenologically, and non-existent
> Ontologically, I guess you mean.  I am not sure I understand well.
>
>
> We live in a constructed reality.
>
>
> The whole physicalness is indeed the arithmetic seen from the internal
> arithmetical beings, but the person attached to them are not arithmetical
> not even analytical (not even third person describable in any way).
>
> I am aware that what I say contradicts 1500 years of (Aristotelian)
> theology, but then it was enforced by 1500 years of argument per authority,
> sometimes violent.
>
> Best,
>
> Bruno
>
>
>
>
>
>
> STAN
>
> On Tue, Mar 20, 2018 at 12:23 PM, Bruno Marchal <marc...@ulb.ac.be> wrote:
>
>> Hi Dai, Hi Carl, Hi colleagues,
>>
>> > On 19 Mar 2018, at 16:22, Dai Griffiths <dai.griffith...@gmail.com>
>> wrote:
>> >
>> > On 15/03/18 10:11, Karl Javorszky wrote:
>> >
>> > >To me, it does not appear necessary to make a distinction between
>> “reality” and “data”
>> >
>> > That's a defensible position, but it does constrain 'reality' to 'that
>> which we can perceive'. Which would rule out the reality of things that we
>> cannot perceive, e.g. explanatory mechanisms, or the insides of black holes.
>>
>> If not the whole of mathematics.
>>
>> To be provocative, I would me more like thinking that the data are an
>> observer tiny distorted part of reality, especially that we can never
>> distinguishes possibly genuine data with hallucinations and dreams.
>>
>> In the computationalist theory, a data is the input to some
>> machine/number program, the execution is the arithmetical semantic of some
>> universal number getting the machine and the data has its input.
>>
>> Now a data can be anything, and can be interpreted, and handled, quite
>> differen```

### Re: [Fis] Meta-observer?

```Loet wrote:

At the level of observers, indeed, a hierarchy may be involved for the
change of focus (although this is empirical  and not necessarily the case).
The communication, however, as a system different from the communicators
may contain mechanisms such as "translation" which make it possible to
redirect.

Koichiro wrote:

At issue must be how something looking like a chain of command could happen
to emerge without presuming such a chain in the beginning. Prerequisite to
its emergence would be the well-being of each participant taken care of
locally, as a replenishable inevitable. That is an issue of the origins of
life. The impending agenda is on something general universal as an object,
and yet concrete particular enough in process.

A comment here:  there are two hierarchies possible in these phenomena: one
is the compositional hierarchy: [higher level [focus of actions [lower
level]]], or [context [action in focus [possibilities]]]. Three levels must
always be in consideration, giving: [permissive ecosystem [participant
actions [enchainment process]]].

The other is the subsumptive hierarchy:  {possibilities -> {choice ->
{refinement}}}. Here a chain might keep going into further modifications,
and the chain branches as well. The context is represented here in the
possibilities.

STAN

On Fri, Mar 2, 2018 at 12:41 AM, Koichiro Matsuno
wrote:

> On 28 Feb 2018 at 10:34 PM, PedroClemente Marijuan Fernadez wrote:
>
> A sort of "attention" capable of fast and furious displacements of the
> focus...  helas, this means a meta-observer or an observer-in-command.
>
>Pedro, it is of course one thing to conceive of a hierarchy of
> observers for our own sake, but quite another to figure out what the
> concrete participants such as molecules are doing out there. They are doing
> what would seem appropriate for them to do without minding what we are
> observing. At issue must be how something looking like a chain of command
> could happen to emerge without presuming such a chain in the beginning.
> Prerequisite to its emergence would be the well-being of each participant
> taken care of locally, as a replenishable inevitable. That is an issue of
> the origins of life. The impending agenda is on something general universal
> as an object, and yet concrete particular enough in process. The richness
> resides within the concreteness down to the bottom.
>
>
>
>Apropos, the communications among the local participants differ from
> computation despite the seemingly concrete outlook of the latter.
> Computation upon the notion of time as the linear sequence of the now
> points is not available to the local participants because of the lack of
> the physical means for guaranteeing the sharing of the same now-point among
> themselves.
>
>
>
>Koichiro Matsuno
>
>
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

```

```Following upon Søren:  Meaning is derived for a system by way of
Interpretation.  The transmitted information has no meaning without
interpretation.

STAN

On Mon, Feb 26, 2018 at 6:26 AM, Søren Brier  wrote:

> Dear  Xueshan
>
>
>
> The solution to the paradox is to go to a metaparadigm that can encompass
> information science as well as linguistics. C.S. Peirce’s semiotics is such
> a paradigm especially if you can integrate cybernetics and systems theory
>  with it. There is a summary of the framework of Cybersemiotics here:
>
> https://pdfs.semanticscholar.org/a5e7/cf50ffc5edbc110ccd08279d6d8b51
> 3bfbe2.pdf
>
>
>
> Cordially yours
>
>
>
>  Søren Brier
>
>
>
> Depart. of Management, Society and Comunication, CBS, Dalgas Have 15
> (2VO25), 2000 Frederiksberg
>
> Mobil 28494162 www.cbs.dk/en/staff/sbrmsc , cybersemiotics.com.
>
>
>
>
>
>
>
> *Fra:* Fis [mailto:fis-boun...@listas.unizar.es] *På vegne af *Xueshan Yan
> *Sendt:* 26. februar 2018 10:47
> *Til:* FIS Group
>
>
>
> Dear colleagues,
>
> In my teaching career of Information Science, I was often puzzled by the
> following inference, I call it *Paradox of Meaning and Information* or
> *Armenia
> Paradox*. In order not to produce unnecessary ambiguity, I state it below
> and strictly limit our discussion within the human context.
>
>
>
> Suppose an earthquake occurred in Armenia last night and all of the main
> media of the world have given the report about it. On the second day, two
> students A and B are putting forward a dialogue facing the newspaper
> headline “*Earthquake Occurred in Armenia Last Night*”:
>
> Q: What is the *MEANING* contained in this sentence?
>
> A: An earthquake occurred in Armenia last night.
>
> Q: What is the *INFORMATION* contained in this sentence?
>
> A: An earthquake occurred in Armenia last night.
>
> Thus we come to the conclusion that *MEANING is equal to INFORMATION*, or
> strictly speaking, human meaning is equal to human information. In
> Linguistics, the study of human meaning is called Human Semantics; In
> Information Science, the study of human information is called Human
> Informatics.
>
> Historically, Human Linguistics has two definitions: 1, It is the study of
> human language; 2, It, also called Anthropological Linguistics or
> Linguistic Anthropology, is the historical and cultural study of a human
> language. Without loss of generality, we only adopt the first definitions
> here, so we regard Human Linguistics and Linguistics as the same.
>
> Due to Human Semantics is one of the disciplines of Linguistics and its
> main task is to deal with the human meaning, and Human Informatics is one
> of the disciplines of Information Science and its main task is to deal with
> the human information; Due to human meaning is equal to human information,
> thus we have the following corollary:
>
> A: *Human Informatics is a subfield of Human Linguistics*.
>
> According to the definition of general linguists, language is a vehicle
> for transmitting information, therefore, Linguistics is a branch of Human
> Informatics, so we have another corollary:
>
> B: *Human Linguistics is a subfield of Human Informatics*.
>
> Apparently, A and B are contradictory or logically unacceptable. It is a
> paradox in Information Science and Linguistics. In most cases, a settlement
> subject, but how should we understand this paradox?
>
>
>
> Best wishes,
>
> Xueshan
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

```

### Re: [Fis] The unification of the theories of information based on the cateogry theory

```Xueshan -- I think one can condense some of your insights hierarchically,
as:

In a system having language, information seemingly may be obtained in other
ways as well. It would be a conceptually broader category. Thus (using the
compositional hierarchy):

[information [language [signal]]]

Meaning that, when a system has language, all information will be
understood or construed by way of linguistic constructs.

(Here I am using ‘signal’ as being more specific than Peirce’s ‘sign’,
where:

[sign [information [...]]] )

Then, more dynamically (using the subsumptive hierarchy):

{language {signal {information}}}

Information in a languaged system is derived by way linguistic formations,
so that, even though it is an extremely broad category, information
(informing) only emerges by way of linguistically informed transformations.

STAN

On Sat, Feb 10, 2018 at 3:21 AM, Xueshan Yan  wrote:

> Dear Colleagues,
>
> I have read the article "The languages of bacteria" which Gordana
> recommended, and has gained a lot of inspiration from it. In combination
> with Sung's comparative linguistics exploration on cell language and human
> language, I have the following learning feelings to share with everyone:
>
> In this article, the author recognized that bacteria have evolved multiple
> languages for communicating within and between species. Intra- and
> interspecies cell-cell communication allows bacteria to coordinate various
> biological activities in order to behave like multicellular organisms. Such
> as AI-2, it is a general language that bacteria use for intergenera
> signaling.
>
> I found an interesting phenomenon in this paper: the author use the
> concept *information* 3 times but the concept *signal* (signal or
> signaling) 55 times, so we have to review the history and application of
> “information” and “signal” in biology and biochemistry, it is helpful for
> us to understand the relationship between language, signal, and information.
>
> The origin of the concept of signal (main the signal transduction) can be
> traced back to the end of the 1970s. But until 1980, biochemist and
> endocrinologist Martin Rodbell published an article titled: “The Role of
> Hormone Receptors and GTP-Regulatory Proteins in Membrane Transduction" in
> *Nature,
> *in this paper he used the "signal transduction" first time. Since then,
> the research on signal transduction is popular in biology and biochemistry.
>
> As for any information transmission system, if we pay more attention to
> its transmission carrier instead of its transmission content, we are used
> to employing "signal transmission" instead of "signal transduction". From
> the tradition of the early use of information concept, the signal
> transduction study of cells is only equivalent to the level of
> telecommunications before 1948. Outwardly, before the advent of Shannon's
> information theory, the central issue of telecommunications is "signal"
> rather than "information". After that, the central issue of
> telecommunications is "information" rather than "signal".
>
> According to the application history of information concept, nearly all
> the essential problems behind the concepts of communication, messenger,
> signal and so on may be information problems. Just as the language problem
> what we are discussing here, our ultimate goal is to analyze the
> information.
>
>
>
> For the same reason, I recommend another two papers:
>
> 1. Do Plants Think?  (June 5, 2012, *Scientific American*)
>
> (http://www.scientificamerican.com/article/do-plants-think-
> daniel-chamovitz/#rd?sukey=fc78a68049a14bb24ce82efd8ef931
> e64057ce6142b1f2f7b919612d2b3f42c07f559f5be33be0881613ccfbf5b43c4b）
>
> 2. Plants Can Think, Feel and Learn  (December 3, 2014, *New Scientist*)
>
> (http://www.newscientist.com/article/mg22429980-400-root-
> intelligence-plants-can-think-feel-and-learn)
>
> From which we can judge whether or not a plants informatics can exists.
>
>
>
> Best wishes,
>
> Xueshan
>
>
>
> *From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
> *On Behalf Of *Sungchul Ji
> *Sent:* Thursday, February 8, 2018 9:10 PM
> *To:* Francesco Rizzo <13francesco.ri...@gmail.com>; Terrence W. DEACON <
> dea...@berkeley.edu>
> *Cc:* Fis,
> *Subject:* Re: [Fis] The unification of the theories of information based
> on the cateogry theory
>
>
>
> Hi Terry,  and FISers,
>
>
>
> Can it be that "language metaphor" is akin to a (theoretical) knife that,
> in the hands of a surgeon, can save lives but, in a wrong hand, can kill?
>
>
>
> All the best.
>
>
>
> Sung
> --
>
> *From:* Francesco Rizzo <13francesco.ri...@gmail.com>
> *Sent:* Thursday, February 8, 2018 2:56:11 AM
> *To:* Terrence W. DEACON
> *Cc:* Fis,; Sungchul Ji
> *Subject:* Re: [Fis] The unification of the theories of information based
> on the cateogry theory
>
>
>
> Caro Terry estensibile a tutti,
>
> è sempre un ```

### Re: [Fis] New Year Lecture

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

STAN

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

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

### Re: [Fis] I do not understand some strange claims

```Jesse, Arturo -- Science is necessarily culture-laden in being motivated
and supported by the interests of the culture affording it.  The observer
cannot escape itself nor its position in the world of possibility. The
information sought by scientific means is already implicit in the
initiation of a search, and will be, given luck and craft, narrowed down by
that search so as to serve as the stepping-off point for the next search.
In this way science progresses toward ever more refined explorations of
cultural desiderata. A nice example is quantum mechanics, as the current
furthest reach of our cultural interest in the ever more minute, which has
already 'paid off'' by an understanding of biology (as well as the building
up of massive and profitable superstructures required by science discourse).

STAN

On Thu, Nov 16, 2017 at 7:39 PM, Jesse David Dinneen <
jesse.dinn...@vuw.ac.nz> wrote:

> Dear Arturo (and greetings to everybody),
>
> Just a few more reasons to be wary of dismissing concepts and thinking
> that science is free of them:
>
> The position you are promoting constitutes a pop view (sometimes called
> the received view or naive view) of science, in which empirical items
> (e.g., measurable things) are taken to be unassailable rather than
> contingently defined and conceived of by science, implicitly or otherwise.
> To call concepts like the previously discussed triad 'useless' ignores the
> fact that they are necessary for meaningful scientific discourse (e.g., you
> cannot talk about observables without having a concept of what they are).
> Scientific discourse is inescapably value- and concept-laden (and full of
> implicit philosophical views), especially so when the terms used are
> implicitly defined or dogmatically defended; if you find these claims
> dubious, the introductory philosophers of science, like Kuhn and Popper,
> might be of interest to you. Further, the theories and observables of past
> scientific discourse have been either abandoned or refined beyond
> recognition despite relative successes in their time (e.g., phlogiston),
> and so it is reasonable to induce that the equivalent items of our time
> will someday meet similar fates -- thus it is risky to put too much faith
> in their objects being somehow more epistemologically sound or reliable
> than the objects of abstract thinking or their study free of concepts,
> philosophical thinking, etc.
>
> surprises me; I am curious to know what harmful social movements you
> foresee being caused by, say, the Bar-Hillel-Carnap Paradox.
>
> Finally, it seems to me that by promoting this view of science, you are
> doing philosophy more than doing science, at least by your own view of the
> latter.
>
> Here I'm not trying to lower science, but defend concepts -- they are
> useful and necessary for scientific discourse, and seem to me very
> appropriate for this particular venue.
>
> Respectfully,
> Jesse David Dinneen
> School of Information Management, Victoria University of Wellington
>
> On Thu, Nov 9, 2017 at 10:11 AM, tozziart...@libero.it <
> tozziart...@libero.it> wrote:
>
>> Dear FISers,
>>
>> science talks about observables, i.e., quantifiable parameters.
>>
>> Therefore, describing the word "information" in terms of philosophers'
>> statements, hypothetical useless triads coming from nowhere, the ridicolous
>> Rupert Sheldrake's account, mind communication, qualitative subjective
>> issues of the mind, inconclusive phenomelogical accounts with an hint of
>> useless husserlian claims, and such kind of amenities is simply: NOT
>> scientific.
>> It could be interesting, if you are a magician or a follower of Ermetes
>> Trismegistus, but, if you are (or you think to be) a  scientist, this is
>> simply not science.
>> Such claims are dangerous, because they are the kind of claims that lead
>> to NO-VAX movements, religious stuff in theoretical physics, Heideggerian
>> metapyhsics.  Very interesting, but NOT science.
>>
>> That's all: 'nuff said.
>>
>> *Arturo Tozzi*
>>
>> AA Professor Physics, University North Texas
>>
>> Pediatrician ASL Na2Nord, Italy
>>
>> Comput Intell Lab, University Manitoba
>>
>> http://arturotozzi.webnode.it/
>>
>>
>> ___
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>>
>>
>
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```

### Re: [Fis] some notes

```Pedro -- Regarding:

could we say that the life cycle itself establishes the eigenvectors of
communication? It is intriguing that maintenance, persistence,
self-propagation are the essential motives of communication for whatever
life entities (from bacteria to ourselves). With the complexity increase
there appear new, more sophisticated directions, but the basic ones
probably remain intact. What could be these essential directions of
communication?

S: It is interesting on this point to note the studied avoidance of serious
discourses to include the "life cycle itself" (i.e.: immaturity
->maturity-> senescence) in any scientific study other than some areas of
biology (gerontology).  One can conclude that we have such a fear of aging
that it has blinded our discourses to this basic fact.

STAN

On Mon, Nov 13, 2017 at 8:30 AM, Pedro C. Marijuan <
pcmarijuan.i...@aragon.es> wrote:

> Dear All,
>
> Herewith some notes on the exchanges of past weeks (sorry, I was away in
>
> 1. Agents & Information. There were very good insights exchanged; probably
> both terms make a fertile marriage. Actually I have been writing about
> "informational entities" or "subjects" as receivers/builders of information
> but taking into account the other disciplines around, "agents" look as the
> most natural companion of information. The only thing I don't quite like is
> that they usually appear as abstract, disembodied communicative entities
> that do not need self-producing. Their communication is free from whatever
> life maintenance...
>
> 2. Eigenvectors of communication. Taking the motif from Loet, and
> continuing with the above, could we say that the life cycle itself
> establishes the eigenvectors of communication? It is intriguing that
> maintenance, persistence, self-propagation are the essential motives of
> communication for whatever life entities (from bacteria to ourselves). With
> the complexity increase there appear new, more sophisticated directions,
> but the basic ones probably remain intact. What could be these essential
> directions of communication?
>
> 3. About logics in the pre-science, Joseph is quite right demanding that
> discussion to accompany principles or basic problems. Actually principles,
> rules, theories, etc. are interconnected or should be by a logic (or
> several logics?) in order to give validity and coherence to the different
> combinations of elements. For instance, in the biomolecular realm there is
> a fascinating interplay of activation and inhibition among the
> participating molecular partners (enzymes and proteins) as active
> elements.  I am not aware that classical ideas from Jacob (La Logique du
> vivant) have been sufficiently continued; it is not about Crick's Central
> Dogma but about the logic of pathways, circuits, modules, etc. Probably
> both Torday and Ji have their own ideas about that-- I would be curious to
> hear from them.
>
> 4. I loved Michel's response to Arturo's challenge. I think that the two
> "zeros" I mentioned days ago (the unsolved themes around the cycle and
> around the observer) imply both multidisciplinary thinking and
> philosophical speculation...
>
> Best wishes--Pedro
>
> -
> Pedro C. Marijuán
> Grupo de Bioinformación / Bioinformation Group
> Instituto Aragonés de Ciencias de la Salud
> Centro de Investigación Biomédica de Aragón (CIBA)
> Avda. San Juan Bosco, 13, planta 0
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.i...@aragon.es
> -
>
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```

### [Fis] agency

```10:20 AM (0 minutes ago)
to Mark
Mark -  In a physical field where many masses are interacting by way of
vectors, agency appears only
if a particular individual mass is discerned by way of discourse. A fox
picks out one chicken for dinner,
the rest scatter anonymously.

STAN
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### Re: [Fis] TR: What is ³Agent²?

```words are metaphors and metaphor literally means to carry across, derived
> from the Greek meta (literally ‘across') and phorein (literally 'to
> carry'). So the word information has been carried across from one domain or
> area of interest to another. It entered the English language as the noun
> associated with the verb 'to inform', i.e. to form the mind. Here is an
> excerpt from my book *What Is Information? *(available for free at
> demopublishing.com):
>
> *"Origins of the Concept of Information - *We begin our historic survey
> of the development of the concept of information with its etymology. The
> English word information according to the Oxford English Dictionary (OED)
> first appears in the written record in 1386 by Chaucer: 'Whanne Melibee
> hadde herd the grete skiles and resons of Dame Prudence, and hire wise
> informacions and techynges.' The word is derived from Latin through French
> by combining the word inform meaning giving a form to the mind with the
> ending “ation” denoting a noun of action. This earliest definition refers
> to an item of training or molding of the mind.” This is why abiotic objects
> have no information as I claimed above because they have no mind that can
> be informed.
>
> I hope that by informing you of the origin of the word information I have
> shed some light on our confusion about what is information and why we have
> so many definitions of it. It might even shed some light for that matter as
> to what is an agent. Got the ticket? If so that makes me a ticket agent. I
> hope you get the joke. all the best - Bob
>
>
>
>
> __
>
>
>
> Robert K. Logan
>
> Prof. Emeritus - Physics - U. of Toronto
>
> Fellow University of St. Michael's College
>
> Chief Scientist - sLab at OCAD
>
>
> www.researchgate.net/profile/Robert_Logan5/publications
>
> https://www.physics.utoronto.ca/people/homepages/logan/
>
>
>
>
>
> On Oct 19, 2017, at 7:11 PM, Terrence W. DEACON <dea...@berkeley.edu>
> wrote:
>
>
>
> AUTONOMOUS AGENCY: The definition I propose for autonomous agency It is
> open to challenge. Of course, there are many ways that we use the term
> 'agent' in more general and metaphoric ways. I am, however, interested in
> the more fundamental conception that these derived uses stem from. I do not
> claim that this definition is original, but rather that it is what we
> implicitly understand by the concept. So if this is not your understanding
> I am open to suggestions for modification.
>
>
>
> I should add that it has been a recent goal of my work to describe an
> empirically testable simplest model system that satisfies this definition.
> Those of you who are familiar with my work will recognize that this is what
> I call an autogenic or teleodynamic system. In this context, however, it is
> only the adequacy of the definition that I am interested in exploring. As
> in many of the remarks of others on this topic it is characterized by
> strange-loop recursivity, self-reference, and physicality. And it may be
> worth while describing how this concept is defined by e.g. Hofstadter, von
> Foerster, Luhmann, Moreno, Kauffman, Barad, and others, to be sure that we
> have covered the critical features and haven't snuck in any "demons". In my
> definition, I have attempted to avoid any cryptic appeal to observers or
> unexamined teleological properties, because my purpose is instead to
> provide a constructive definition of what these properties entail and why
> they are essential to a full conception of information.
>
>
>
> CENTRALITY OF NORMATIVE PROPERTIES: A critical factor when discussing
> agency is that it is typically defined with respect to "satisfaction
> conditions" or "functions" or "goals" or other NORMATIVE properties.
> Normative properties are all implicitly teleological. They are irrelevant
> to chemistry and physics. The concept of an "artificial agent" may not
> require intrinsic teleology (e.g. consider thermostats or guidance systems
> - often described as teleonomic systems) but the agentive properties of
> such artifacts are then implicitly parasitic on imposed teleology provided
> by some extrinsic agency. This is of course implicit also in the concepts
> of 'signal' and 'noise' which are central to most information concepts.
> These are not intrinsic properties of information, but are extrinsically
> imposed distinctions (e.g. noise as signal to the repair person). So I
> consider the analysis of agency and its implicit normativity to be a
> fundamental issue to be resolved in our analysis of information. Though we
> can still bracket any con```

### Re: [Fis] What is “Agent”?

```Here is an interesting recent treatment of autonomy.

Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical

and Theoretical Enquiry (History, Philosophy and Theory of the Life
Sciences 12);

Springer, Dordrecht, 2015, xxxiv + 221 pp., \$129 hbk, ISBN 978-94-017-9836-5

STAN

On Thu, Oct 19, 2017 at 11:44 AM, Terrence W. DEACON
wrote:

> AN AUTONOMOUS AGENT IS A DYNAMICAL SYSTEM ORGANIZED TO BE CAPABLE OF
> INITIATING PHYSICAL WORK TO FURTHER PRESERVE THIS SAME CAPACITY IN THE
> CONTEXT OF  INCESSANT EXTRINSIC AND/OR INTRINSIC TENDENCIES FOR THIS SYSTEM
>
>
> THIS ENTAILS A CAPACITY TO ORGANIZE WORK THAT IS SPECIFICALLY CONTRAGRADE
> TO THE FORM OF THIS DEGRADATIONAL INFLUENCE, AND THUS ENTAILS A CAPACITY TO
> BE INFORMED BY THE EFFECTS OF THAT INFLUENCE WITH RESPECT TO THE AGENT’S
> CRITICAL ORGANIZATIONAL CONSTRAINTS.
>
> On Wed, Oct 18, 2017 at 6:00 PM, Koichiro Matsuno
> wrote:
>
>> On 19 Oct 2017 at 6:42 AM, Alex Hankey wrote:
>>
>>
>>
>> the actual subject has to be non-reducible and fundamental to our
>> universe.
>>
>>
>>
>>This view is also supported by Conway-Kochen’s free will theorem
>> (2006). If (a big IF, surely) we admit that our fellows can freely exercise
>> their free will, it must be impossible to imagine that the atoms and
>> molecules lack their share of the similar capacity. For our bodies
>> eventually consist of those atoms and molecules.
>>
>>
>>
>>Moreover, the exercise of free will on the part of the constituent
>> atoms and molecules could come to implement the centripetality of Bob
>> Ulanowicz at long last under the guise of chemical affinity unless the case
>> would have to forcibly be dismissed.
>>
>>
>>
>>This has been my second post this week.
>>
>>
>>
>>Koichiro Matsuno
>>
>>
>>
>>
>>
>>
>>
>> *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Alex
>> Hankey
>> *Sent:* Thursday, October 19, 2017 6:42 AM
>> *To:* Arthur Wist ; FIS Webinar <
>> Fis@listas.unizar.es>
>> *Subject:* Re: [Fis] What is “Agent”?
>>
>>
>>
>> David Chalmers's analysis made it clear that if agents exist, then they
>> are as fundamental to the universe as electrons or gravitational mass.
>>
>>
>>
>> Certain kinds of physiological structure support 'agents' - those
>> emphasized by complexity biology. But the actual subject has to be
>> non-reducible and fundamental to our universe.
>>
>>
>>
>> Alex
>>
>>
>>
>>
>>
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>>
>>
>
>
> --
> Professor Terrence W. Deacon
> University of California, Berkeley
>
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```

### Re: [Fis] Heretic

```Bob -- Your classification of information-related concepts:

• Data are the pure and simple facts without any particular structure or
organization, the basic atoms of information,

• Information is structured data, which adds meaning to the data and gives
it context and significance,

• Knowledge is the ability to use information strategically to achieve
one's objectives, and

• Wisdom is the capacity to choose objectives consistent with one's values
and within a larger social context

slightly reworked, can be understood as a development using a subsumptive
hierarchy:

{facts {data -->information {knowledge {understanding}

with {lower {higher}}

STAN

On Thu, Oct 5, 2017 at 12:39 PM, Bob Logan
wrote:

> Dear Arturo - I enjoyed your expression of your opinion  because of its
> directness and honesty even though I do not quite agree with everything you
> said. I enjoyed it because it provoked the following thoughts.
>
> Yes you are right there seems to be a variety of opinions as to just what
> information is. All of them are correct and all of them are wrong including
> mine which I will share with you in a moment. They are right in that they
> describe some aspect of the notion of information and they are all wrong
> because they are attempting to be precise and that is not possible. All
> words including the word ‘information’ are metaphors and a metaphor cannot
> be right or wrong - it can only be illuminating if inspired or irrelevant
> if too narrow. I am afraid caro Arturo that there cannot be a scientific
> definition of ‘information’ because definitions cannot be falsified and as
> Karl Popper once suggested for a proposition to be scientific it has to be
> falsifiable. Of course this is Popper’s definition of science so some may
> disagree. So I am with you so far. But where I have to disagree is when you
> call the activity of trying to define information a useless activity. I
> think it is useful if only for us to see the various dimensions of this
> notion.
>
> Now as promised my thoughts re: what is information? In fact I have
> written a whole book on the subject which I invite all FISers to read free
> of charge as it is available in an open access format at
> demopublishing.com
> The availability of the book for free is part of an experiment in which I
> wanted to explore if a book could be a two-way form of communication
> my book and if you do please honour me with a comment or two as the Web
> site you access the book at also has provisions for you feedback. PS - The
> book is also available in hard copy from Amazon.
>
> So now for my definition of information as can be found in the book.
>
> • Data are the pure and simple facts without any particular structure or
> organization, the basic atoms of information,
>
> • Information is structured data, which adds meaning to the data and gives
> it context and significance,
>
> • Knowledge is the ability to use information strategically to achieve
> one's objectives, and
>
>  • Wisdom is the capacity to choose objectives consistent with one's
> values and within a larger social context
>
> In the book I also quote T. S. Eliot whose lines of poetry provide another
> perspective on wisdom, knowledge and information
>
> Where is the wisdom we have lost in knowledge?
> Where is the knowledge we have lost in information? ­– TS Eliot
>
> My definition of information as well as that of TS Eliot does not
> encompass the notion of physicists who talk about information in terms of
> Wheeler’s "it from bit” idea.
> For me inanimate objects have no information because they have no choice.
> They slavishly follow the laws of physics. Only biological, living
> organisms have information because they have choice and information is that
> which allows them to make their choices. And information is that which they
> perceive through their senses from the simplest bacteria to us humans that
> ee cummings described as "fine specimen(s) of hypermagical
> ultraomnipotence”   So this is my second notion of what is ‘information’.
>
> Even a book is not a form of information. It is the record of information
> created by its author and it is a medium that allows its readers to recreate
> that original information of its author. From a McLuhan perspective we could
>
> also ask is information the medium or the message. McLuhan would say they are
> the same since he said 'the medium is the message'. And he would also agree
> that it is the reader that recreates information when the book
>
> is read since he also said “the user is the content”.
>
> Since composing this response a post from Lars-Göran Johansson appeared with
> which I am in agreement
>
> Best wishes to all - Bob Logan
>
>
>
> __
>
> Robert K. Logan
> Prof. Emeritus - Physics - U. of Toronto
> Fellow University of St. Michael's College
> Chief Scientist - sLab at OCAD
> ```

```Pedro wrote:

>Putting it differently, the hierarchies between scientific disciplines
were fashionable particularly in the reductionism times; but now
fortunately those decades (70s, 80s) are far away. Actually, the new views
taking shape are not far from the term "knowledge recombination" that
appears in some of the principles discussed.

I would like to rebut this put-down by pointing out that reduction (while
still meaningful) is no longer the sole burden of hierarchical
formulations. Rather, the major interesting point is that the disciplines
‘higher’ up in the hierarchy:

{physics {chemistry {biology {sociology, with (lower {higher}}

provide context for the lower ones. For example, while chemical actions can
be observed to exist, putatively, outside of a biological context, that
chemistry in our universe must have been organized in such a way as to
potentially give rise to biology. That is, biology, and sociology were
operative implicitly before they existed in fact -- as attractors. Thus,
such top-down influences must have been active in OUR universe during its
inception, as contextualizations (uninfluenced universes cannot be shown to
exist!).  Anything must happen somewhere. Possibly the best evidence for
this has already emerged in the observations of QM, as an implication of
the (sometimes currently disparaged) concept of the role of the observer. I
think it unproblematic that Information can flow from a higher level to a
lower, as a constraint. Indeed the field of QM, with all of its very
expensive equipment, is a good example of this.

Yes, I appear to be arguing for a scientific role for Final Cause.  For
example, if a naturalist goes out to a forested region to study, say, birds
of paradise, where can these be found that has not already been modified by
humans (even by the camera)? Is information science intrinsically opposed
to to finality?

STAN
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```

### [Fis] Pedro's 10 Theses

```Here I indicate my understanding of Pedro's statements on information
STAN

10 PRINCIPLES OF INFORMATION SCIENCE

1. Information is information, neither matter nor energy.

S: I have information as a perceptible result of interaction,
which may be embodied in matter and/or energy

Information is comprehended into structures, patterns, messages, or flows.

S: Agreed

3. Information can be recognized, can be measured, and can be  processed

(either computationally or non-computationally).

S: If an interaction has an effect, that effect can be converted
to other embodiments, resulting in informing

4. Information flows are essential organizers of life's self-production

processes--anticipating, shaping, and mixing up with the accompanying

energy flows.

S: Life, as an information-guided local process-embodiment,
transforms other forms by extracting usable energy and materials from them.

5. Communication/information exchanges among adaptive life-cycles underlie

the complexity of biological organizations at all scales.

S: Information, as such, has no scale restriction. However,
informed processes in living systems proceed independently at many scales.

6. It is symbolic language what conveys the essential communication

exchanges of the human species--and constitutes the core of its "social

nature."

S: Informing has been constructed as a basic tool among humans.

7. Human information may be systematically converted into efficient

knowledge, by following the "knowledge instinct" and further up by

applying rigorous methodologies.

S: Among humans information is used to construct and effect
technologies.

8. Human cognitive limitations on knowledge accumulation are partially

overcome via the social organization of "knowledge ecologies."

S: Humans have methods for sharing information.

9. Knowledge circulates and recombines socially, in a continuous

actualization that involves "creative destruction" of fields and

disciplines: the intellectual Ars Magna.

S: Methods of sharing information among humans have become
developed as discourses

10. Information science proposes a new, radical vision on the information

and knowledge flows that support individual lives, with profound

consequences for scientific-philosophical practice and for social

governance.

S: Information Science proposes to embody a special
understanding of informational transactions as an acknowledged discourse.
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```

### [Fis] Fwd: Mazur/HuffPost: A Chat with Information Scientist Pedro Marijuán

```-- Forwarded message --
From: Suzan Mazur
Date: Sun, Aug 7, 2016 at 8:32 AM
Subject: Mazur/HuffPost: A Chat with Information Scientist Pedro Marijuán
To: szn...@aol.com

My interview with Pedro Marijuán, FYI. -- *Suzan*
http://www.huffingtonpost.com/suzan-mazur/a-chat-with-inform
ation-s_b_11212594.html
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```

### Re: [Fis] _ Reply to Annette (A Priori Modeling)

```Entropy

Regarding:
> So I see it that you confirm to Shannon´s interpretation of entropy as
actually being information <
Well, in essence we may agree, but I would call this an unfortunate choice
of words. “Information," I think, has come to mean so many things to so
many people that it is *nearly* a useless term. Even though I use this term
myself, I try to minimize its use. I would say that I agree with Shannon’s
view of signal entropy as a *type* of information – and then extend that
concept using type theory, to include “meaningful” roles. Only when taken
as a whole does “information” exist, within my framing.

S: It has been shocking to me that many info-tech persons use the word
'information' when what they mean is Shannon's 'information carrying
capacity' or the word 'entropy' when they mean Shannon's 'informational
entropy', referring to variety.

STAN

On Wed, Jun 22, 2016 at 5:41 AM, Marcus Abundis <55m...@gmail.com> wrote:

> In an online exchange, Annette raises a few points and questions that I
> summarize below.
> ===
> My short answer is that I define entropy as "material variation" of any
> type, as clarified in paper #2 and detailed starting on page 5 (actually
> named on page 6). This definition is admittedly generic/vague, for a few
> reasons:
>   a) many "types of meaning" (or entropy, if you wish) must be framed and
> then joined. I name three minimum types of meaning/entropy in paper #2.
> This multitude requires that a generic term first be named if an UTI is to
> be developed (point 1 in the introductory text).
>   b) noise is itself informational in a Darwinian role as “demise.” I
> believe this departs from most informational notions, where noise is seen
> as the opposite of information. This view also accommodates an inverse,
> where one eventually “makes sense” of nominally chaotic events.
> As such, I name an existential ground Generic Entropy, and the “tendency
> to symmetric dispersal,” within that ground, “material entropy.” And so,
> “material variation” (of any type) is meant to capture the entirety of
> those entropic roles. Lastly, I find the notion of “pure symmetry” a useful
> scientific fiction, but still a fiction in the context of true empiric
> models (point 8 in the introductory text).
>
> > So the different entropies you are using in your video point to
> different options to organize <
> > elements in a way that they generate recognizable (and therefore to a
> degree similar) <
> > information out of those elements? <
> Here, *options* and *recognizable* are the key terms. As you note, I am
> using a different (novel?) notion of “entropy,” beyond even the novel way
> in which Shannon did, and thus (hopefully) extend Shannon's view. The most
> reductive aspect here is “the element” (i.e., a “fulcrum,“ a “load,” a
> “bit,” etc. [re paper #4]). Then, inter-RELATED *element sets,* depending
> on their order (innate functioning or dis-functioning), convey a specific
> role (signal or noise). It is this RELATING of singular elements (there are
> many *options*) that conveys specific meaning/functioning/logic/order. This
> meaningful relating can equally convey *recognizable* “types of order” or
> “types disorder” (e.g., many “types of screws” exist, each with unique
> functional advantages and disadvantages, or uses and mis-uses – a machine
> screw works poorly in wood). Finally, a “recognizably deformed screw” (a
> use-less *option*) must also be accounted for within this continuum. This
> notion of related data echoes the idea already noted in the exchange with
> Antonio.
>
> > So I see it that you confirm to Shannon´s interpretation of entropy as
> actually being information <
> Well, in essence we may agree, but I would call this an unfortunate choice
> of words. “Information," I think, has come to mean so many things to so
> many people that it is *nearly* a useless term. Even though I use this term
> myself, I try to minimize its use. I would say that I agree with Shannon’s
> view of signal entropy as a *type* of information – and then extend that
> concept using type theory, to include “meaningful” roles. Only when taken
> as a whole does “information” exist, within my framing.
>
> Also, the notion of stability (as necessary for meaning) you emphasize I
> find helpful but also limiting. I tend to think of  *everything* as pro tem
> except for perhaps the Standard Model and the Periodic Table (addressed in
> paper #2; Lee Smolin may disagree?). Within type theory the central
> question becomes “At what point/level(s) does material variation
> (“entropy”) break down or fail?”, and how and why does it fail? For me,
> this is a more useful way of viewing things – using stability is too much
> like The Denial of Death (Ernest Becker). This requires us to look beyond
> thermodynamics for answers. I believe thermodynamics is historically
> stressed as it is the closest we have to a “hard science” that we might
> ```

### Re: [Fis] Fw: "Mechanical Information" in DNA

```Regarding your last posting, I agree, and would formulate the following
subsumption hierarchy:

(thermodynamic energy flows {Shannon information theory {Peircean
semiotics}}}

STAN

On Thu, Jun 9, 2016 at 10:31 AM, Mark Johnson  wrote:

> Dear all,
>
> Is this a question about counting? I'm thinking that Ashby noted that
> Shannon information is basically counting. What do we do when we count
> something?
>
> Analogy is fundamental - how things are seen to be the same may be more
> important than how they are seen to be different.
>
> It seems that this example of DNA is a case where knowledge advances
> because what was once thought to be the same (for example, perceived
> empirical regularities in genetic analysis) is later identified to be
> different in identifiable ways.
>
> Science has tended to assume that by observing regularities, causes can be
> discursively constructed. But maybe another way of looking at it is to say
> what is discursively constructed are the countable analogies between
> events. Determining analogies constrains perception of what is countable,
> and by extension what we can say about nature; new knowledge changes that
> perception.
>
> Information theory (Shannon) demands that analogies are made explicit -
> the indices have to be agreed. What do we count? Why x? Why not y?
> otherwise the measurements make no sense. I think this is an insight that
> Ashby had and why he championed Information Theory as analogous to his Law
> of Requisite Variety (incidentally, Keynes's Treatise on Probability
> contains a similar idea about analogy and knowledge). Is there any reason
> why the "relations of production" in a mechanism shouldn't be counted?
> determining the analogies is the key thing isn't it?
>
> One further point is that determining analogies in theory is different
> from measuring them in practice. Ashby's concept of cybernetics-as-method
> was: "the cyberneticist observes what might have happened but did not".
> There is a point where idealised analogies cannot map onto experience. Then
> we learn something new.
>
> Best wishes,
>
> Mark
> --
> From: Loet Leydesdorff
> Sent: ‎09/‎06/‎2016 12:52
> To: 'John Collier' ; 'Joseph Brenner'
> ; 'fis'
> Subject: Re: [Fis] Fw:  "Mechanical Information" in DNA
>
> Dear colleagues,
>
>
>
> It seems to me that a definition of information should be compatible with
> the possibility to measure information in bits of information. Bits of
> information are dimensionless and “yet meaningless.” The meaning can be
> provided by the substantive system that is thus measured. For example,
> semantics can be measured using a semantic map; changes in the map can be
> measured as changes in the distributions, for example, of words. One can,
> for example, study whether change in one semantic domain is larger and/or
> faster than in another. The results (expressed in bits, dits or nits of
> information) can be provided with meaning by the substantive theorizing
> about the domain(s) under study. One may wish to call this “meaningful
> information”.
>
>
>
> I am aware that several authors have defined information as a difference
> that makes a difference (McKay, 1969; Bateson, 1973). It seems to me that
> this is “meaningful information”. Information is contained in just a series
> of differences or a distribution. Whether the differences make a difference
> seems to me a matter of statistical testing. Are the differences
> significant or not? If they are significant, they teach us about the
> (substantive!) systems under study, and can thus be provided with meaning
> in the terms of  studying these systems.
>
>
>
> Kauffman *et al*. (2008, at p. 28) define information as “natural
> selection assembling the very constraints on the release of energy that
> then constitutes work and the propagation of organization.” How can one
> measure this information? Can the difference that the differences in it
> make, be tested for their significance?
>
>
>
> Varela (1979, p. 266) argued that since the word “information” is derived
> from “in-formare,” the semantics call for the specification of a system of
> reference to be informed. The system of reference provides the information
> with meaning, but the meaning is not in the information which is “yet
> meaningless”. Otherwise, there are as many “informations” as there are
> systems of reference and the use of the word itself becomes a source of
> confusion.
>
>
>
> In summary, it seems to me that the achievement of defining information
> more abstractly as measurement in bits (*H = -* Σ *p log(p)*) and the
> availability of statistics should not be ignored. From this perspective,
> information theory can be considered as another form of statistics (entropy
> statistics). A substantive definition of information itself is no longer
> meaningful (and perhaps even ```

### Re: [Fis] Fwd: Vol 25, #32, Nature of Self

```Lou, Alex -- Here is another use of set theoretical brackets (the
subsumption hierarchy in evolution):  {  ? -> {physical world -> {material
world -> {biological world -> {social world }

STAN

On Sat, Apr 30, 2016 at 2:14 AM, Louis H Kauffman  wrote:

> On Pedro’s recommendation, I am forwarding this exchange to the list.
> Best,
> Lou
>
> Begin forwarded message:
>
> *From: *Louis H Kauffman
> *Subject: **Re: Vol 25, #32, Nature of Self*
> *Date: *April 29, 2016 at 12:12:26 PM EDT
> *To: *Alex Hankey
> *Cc: *"Pedro C. Marijuan"
>
> Dear Alex,
> In set theory, the empty set can be regarded as ‘framing nothing’.
> Thus it is denoted by an empty container {  }.
> The properties of the container are not relevant, only that ‘it’ manages
> the act of containment.
> “We therefore take the form of distinction for the form.”
> From there, one generates all the multiplicities in mathematics by further
> acts of framing.
> {  }
> { { } }
> { { }, { { } } }
> If we said this in LOF it would be essentially the same, but parsimonious
> in that the comma as an extra distinction would not be needed.
> If A is a set, then {A} is another set obtained by the act of framing. We
> see it all as ‘framing nothing’ when the sets are traced back to their
> empty origins as in
> the layers of an onion. Some layering might have to be traced back forever
> alas as in {…}. This is why set theorists are not happy to have
> sets that are members of themselves at the foundation. Nevertheless, in
> order to have language at all, self-reference is necessary. In LOF the mark
> < > is seen to be a distinction and to refer to a distinction and so refers
> to itself.
> At that point one realizes that in the form, the mark and the reader or
> writer or observer are identical. Tat tvam asi.
> Best,
> Lou
>
> On Apr 29, 2016, at 5:47 AM, Alex Hankey  wrote:
>
> RE 1 Louis Kauffman: Emptiness is form and form is emptiness. The form we
> take to exist arises from framing nothing.
>
> RE 2: The objects of our thought and perception are so laden with the
> names and symbols that have been shifted to them, that their ?original
> nature? is nearly invisible.
>
> ME 1: Many philosophers of the East, such as Nagarjuna and Adishankara
> agree that when one realizes that the real 'Self' has no form (and no
> history of change) that this frees the embodied soul from being trapped in
> forms that get reincarnated in time. It is the Ultimate Liberating
> Realization!
>
> The Maharishi International University mathematician, Michael Weinless,
> formerly an Asst Prof at Harvard, was correspondingly fond of RusselL's
> distinction between ϕ and [ϕ].
>
> Is this the same as what you are referring to, the 'framing of nothing'?
>
> ME(2): I suspect that the cognitions of a fully enlightened person is
> acutely aware of the additional nonsense that has surrounded the original
> simplicity in such cases.
>
> E.G. In the webinar, I became acutely aware of many layers of academic
> comment / prejudice etc. that surround almost every seemingly innocent
> discussion question.
>
> --
> Alex Hankey M.A. (Cantab.) PhD (M.I.T.)
> Distinguished Professor of Yoga and Physical Science,
> SVYASA, Eknath Bhavan, 19 Gavipuram Circle
> Bangalore 560019, Karnataka, India
> Mobile (Intn'l): +44 7710 534195
> Mobile (India) +91 900 800 8789
>
>
> 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences,
> Mathematics and Phenomenological Philosophy
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
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```

### Re: [Fis] Fis 25 / 9

```RE: The organization of bodies of knowledge in the sciences takes place at

another level than the integration of cognition in the body of an

individual. One cannot reduce the one level to the other, in my opinion.

Which research program of these two has priority? How do they relate ?

potentially differently ? to information?

ME: My Cambridge colleague, Madan Thangavelu, holds that the structure of
knowledge in both human brains (and human organizations), and in' bodies of
knowledge' in the sciences, is fractal.

STAN: I don’t think that “fractal” answers Bob’s question. In fractal
organization there are no ‘levels’ as used by Bob.  Bob’s “levels” would
exist in a compositional hierarchy, wherein levels cannot communicate in an
interactional sense, but, rather, communicate indirectly, with the upper
level imposing boundary conditions upon a lower, while a lower provides raw
materials that might become organized by those boundary conditions.

STAN

On Wed, Apr 6, 2016 at 1:30 AM, Alex Hankey  wrote:

> RE: The organization of bodies of knowledge in the sciences takes place at
> another level than the integration of cognition in the body of an
> individual. One cannot reduce the one level to the other, in my opinion.
> Which research program of these two has priority? How do they relate ?
> potentially differently ? to information?
>
> ME: My Cambridge colleague, Madan Thangavelu, holds that the structure of
> knowledge in both human brains (and human organizations), and in' bodies of
> knowledge' in the sciences, is fractal.
>
> It is certainly true that the structure of creative ideas and new projects
> emerging from individuals and corporations has a fractal kind of
> distribution, and as a consequence, has to be assessed using a Herfyndahl
> index rather that the mean and standard deviation of a normal distribution,
> or their analogues for experimentally encountered non-normal data
> distributions. (Better the square root of the Herfyndaho index, since this
> can be additive when combining distributions.)
>
> --
> Alex Hankey M.A. (Cantab.) PhD (M.I.T.)
> Distinguished Professor of Yoga and Physical Science,
> SVYASA, Eknath Bhavan, 19 Gavipuram Circle
> Bangalore 560019, Karnataka, India
> Mobile (Intn'l): +44 7710 534195
> Mobile (India) +91 900 800 8789
>
>
> 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences,
> Mathematics and Phenomenological Philosophy
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
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```

### [Fis] _ Re: _ Re: _ DISCUSSION SESSION: INFOBIOSEMIOTICS

```All --  There is the World, and there is Nature, our model of the world.
Nature is based in (usually one kind of) logic, even though there is scant
evidence that the world operates only or mostly logically. The evidence
that there is is found in successful applications of engineering and
technology, leaving most aspects of the world (including much of human
mentality) un-modeled. Information is a logical notion. It exists in (as I
see it) three levels in a subsumptive hierarchy -- {variety {choice
{interpretation/effect}}}. So information is part of our model of the
world. Since our species has been (almost excessively) successful, we can
be assured that the world does have logical properties, to which our
mentality has become adapted. However, aspects of the world that are (one
might say) ‘illogical’ appear to be closing in upon us. These aspects
include, I think, what Søren is trying to capture in his thinking.

STAN

On Sun, Apr 3, 2016 at 4:49 AM, Mark Johnson  wrote:

> Dear Soren, Lou and Loet,
>
> I can appreciate that Bateson might have had it in for hypnotists and
> missionaries, but therapists can be really useful! Had Othello had a
> good one, Desdemona would have lived – they might have even done some
> family therapy!
>
> More deeply, Bateson’s highlighting of the difference between the way
> we think and the way nature works is important. How can a concept of
> information help us to think in tune with nature, rather than against
> it?
>
> Loet’s description of social systems as encoded systems of
> expectations within which selections are made is helpful. A concept of
> information is such a selection. But we live in a world of finite
> resources and our expectations form within what appear to be real
> limits: Othello saw only one Desdemona. Similarly, there appears to be
> scarcity of food, money, shelter, safety, education, opportunity for
> ourselves and for our children upon whose flourishing we stake our own
> happiness. These limits may be imagined or constructed, but their
> effects are real to the point that people will risk their lives
> crossing oceans, fight and kill for them. This is a result of how we
> think: it leads to hierarchy, exclusion and the production of more
> scarcity. Nature appears not to work like this.
>
> If we accept that the way we think is fundamentally different from the
> way nature works, how might a concept of information avoid
> exacerbating the pathologies of human existence? Wouldn’t it just turn
> us into information bible-bashers hawking our ideas in online forums
> (because universities are no longer interested in them!)? Would new
> metrics help? Or would that simply create new scarcity in the form of
> a technocratic elite? Or maybe we’re barking up the wrong tree. Maybe
> it’s not “information” at all (whatever that is) – or maybe it’s “not
> information”.
>
> I like “not information” as the study of the constraints within which
> our crazy thinking takes place because it continually draws us back to
> what isn't thought. Without wanting to bash any bibles, Bateson got
> this - see for example the chapter in Steps on "A Re-examination of
> Bateson's Rule". Good therapists get it too. I don't know Peirce well
> enough... Which leads me to a question: “What are the criteria for a
> good theory of information?”
>
> Best wishes,
>
> Mark
>
> On 3 April 2016 at 07:50, Loet Leydesdorff  wrote:
> > Dear Soren,
> >
> >
> >
> > In my opinion, there are two issues here (again J ):
> >
> >
> >
> > 1. the issue of non-verbal (e.g., bodily) communication;
> >
> > 2. the meta-biological or transdisciplinary integration vs. the
> > differentiation among the disciplines.
> >
> >
> >
> > Ad 1. Although I don’t agree with Luhmann on many things, his insistence
> > that everything communicated among humans is culturally coded, is fully
> > acceptable to me. “Love” is not a counter-example. Unlike animals, our
> > behavior is regulated by codes of communication. Preparing "Love” as a
> > passion, Luhmann spent months in the Bibliotheque Nationale in Paris
> > the emergence of romantic love in the literature of the early 18th
> century.
> > A similar intuition can be found in Giddens’ book “The Transformation of
> > Intimacy”. Of course, one sometimes needs bodily presence; Luhmann uses
> here
> > the concept of “symbiotic mechanisms”; but this is only relevant for the
> > variation. The selection mechanisms – which impulses are to be followed –
> > are cultural. Among human beings, this means: in terms of mutual and/or
> > shared expectations. The realm of expecting the other to entertain
> > expectations, shapes a “second contingency” which is otherwise absent in
> the
> > animal kingdom. (If you wish, you can consider it as a function of the
> > cortex as a symbiotic mechanism.)
> >
> >
> >
> > This special status of human society should make us resilient against
> using
> > biological metaphors. ```

### [Fis] _ Biology

```Pedro -- You are right to look dubiously at the achievement of neoDarwinism
as the sole theory of biology.  What is missing (and it was realized
dissipative structures develop -- immaturity followed by a short maturity
followed by senescence -- and this was not escaped when the genetic system
was incorporated, creating living dissipative structures. Development is a
material law of nature, to be added to the underlying physical laws in the
case of dissipative structures. Evo-Devo is a currently burgeoning part of
biology discourse aimed at replacing ‘random mutation’ as the source of new
directions with material divergences occurring during ontogeny. These
reflect material tendencies that can not always be suppressed by genetic
information guidance. They might also in some way reflect choices made by a
developing system. This approach will result in bringing in a major fact of
biological evolution long ignored by neoDarwinians because their
explanatory tool kit could simply bot explain it -- convergent evolution.

STAN
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```

### Re: [Fis] Origin?

```Marcus -- You have an interesting point regarding plants and
phenomenology.  Their behavior occurs over a time scale where we
phenomenologists see nothing happening. This slow time scale was
illuminated by non-phenomenological science studies, while also inquiring
into faster-than-phenomenological time scale events. Is phenomenology to be
grounded in our animal time scale only? Or, in what way or sense can
phenomenology transcend that scale?

STAN

On Mon, Feb 22, 2016 at 12:05 AM, Marcus Abundis <55m...@gmail.com> wrote:

> Dear Stanley & Loet,
> Gentlemen, when you speak of "origin" I am unsure of what *exactly*
> you have in mind. Is it the "origin of the capacity for movement" that you
> think about? The origin of life, itself, along with all its causal roles?
> Or?
> > Then, many of the living do not ‘move’. . . Plants move slowly by
> growth. How could a phenomenologist view this at all?<
> I think studying *differential movement* could fall within
> phenomenology, but explaining the *origination* of autonomous movement,
> would not. Also, it seems (to me) a bit unreasonable to think such an
> origination (origin of life) narrative would be addressed in this group. Or
> do I mistake your meaning, or the group's ultimate aim? Thanks!
>
> Maxine,
> I am unclear from your extended abstract on what exactly you aim to
> accomplish in the study you present. Also, are we to read the
> "Phenomenology and Life Sciences" piece as well? I read its abstract and
> its mention of "coordinated dynamics" seemed to say "yes!" but I am unsure.
> The emphasis you seem to offer in "Phenomenology and Evolutionary
> Biology" I find interesting. Also, your mention of "static" and "genetic"
> aspects along with movement. To my mind this points to kinematics, statics,
> and dynamics in a more directly mechanical sense – but which you now wish
> to tie to evolutionary biology? Is that correct? I find that an interesting
> line of thought.
> Also, I like Pedro's notion of a connection between dance and mate
> selection. Dance then being a display behavior demonstrating an
> advantageous capacity for navigating the evolutionary landscape.
> Still, I find what you present a bit "too raw" and I am not exactly
> sure how I should view the material. For example jumping form
> dance/movement to teeth leaves me with a big gap in joining the two. I get
> the sense that you aim to close "a gap" but I am not clear on how exactly
> you do so. "Where did the notion of a tool come from?" This is an important
> question, but how is it precisely answered or addressed? Do you attribute
> the entire genesis of "six simple machines" all to teeth?
> Lastly, I too work in this area and I am just now finishing (very
> rough draft) a piece that looks at this issue. I agree that it is an
> overlooked area of study. I am happy to share what I have wth you, if you
> might find it of interest.
>
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>
>
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```

### [Fis] _ Re: Fw: Five Momenta. Five Itineraries

```Bruno, Joseph -- The unity of the sciences comes from the fact that one
understands sociality by way of biology, and one understands biology by way
of chemistry, and then one understands chemistry by way of physics. Thus,
the subsumptive hierarchy:

{physics {chemistry {biology {sociality

Comte, I think first showed us this.

STAN

On Fri, Feb 5, 2016 at 10:31 AM, Bruno Marchal  wrote:

> Dear Loet,
>
> Sorry for bumping this old post, but I cannot resist (I tried!) to add my
> grain of salt.
>
>
> On 21 Oct 2015, at 08:37, Loet Leydesdorff wrote:
>
> Self-reference is a key principle in art and humor and it may also be a
> key component of the structured coherence in science Pedro and we are
> seeking.
>
> Dear Joseph:
>
> Do not count me in to the “we”, please. In my opinion, these “unity of
> science” principles are outdated. At issue is to specify how the sciences
> and specialties are different; in which respects and why? Obviously, the
> boundaries are fuzzy, since what may seem far distanced from one
> perspective can be nearby from another (e.g. in terms of the metrics used
> for the measurement such as in the case of biometrics and econometrics).
>
> These distinctions are not to be identified into a single “self” of the
> self-reference, but to be dissolved (differentiated) in discourse. They are
> carried by the communication in science & technology studies or more
> broadly (since including the science/society interface) in the information
> sciences. The “self” is not transcendental to these discourses, but
> reflexive insofar as one has the communicative competencies to listen and –
> if so wished -- to participate.
>
> The distinctions (such as the ones between your five schemes) may be
> useful heuristics. The puzzles have then to be specified.
>
>
>
> I think that I might agree with Pedro and Joseph. The unity of science
> should be preserved, despite this is hard to do when specialities lost
> themselves in gigantic territories.
> This eventually made the search of unity in science into a "new' science,
> or perhaps, if we assume the conceptually strong hypothesis of Mechanism
> (Descartes/Turing) into the oldest of all sciences: theology.
>
> In that case we can define a straitforward notion of self: the
> representation of the body of the machine in its brain. Descartes sought
> fort his without finding it, and Hanz Driesch, with embryology in mind,
> pretended this could not exist, due to the apparent infinite looping most
> naïve attempts seem to lead to. But von Neuman, and more conceptually
> Stephen Kleene solved that problem. John Case solved the more complex
> embryological problem. The basic idea is contained in the Dx =>T(xx) trick:
> DD will give (=>) T(DD), that is the transformation T on itself.
>
> And I agree that there is nothing transcendental in that notion of self.
>
> But that notion is third person descriptible, which is not the case for
> the first person "I", which is the one who know, notably when it has some
> headache, plain or some pleasure.
>
> To get this one, Theatetus suggested to attach the "believer" ([]p) with
> "truth" (p), and we know today that such notion of truth, and thus of
> knowledge ([]p & p) is transcendental.
>
> It is transcendental in two sense: truth (even just the arithmetical
> truth) is not exhaustible.
> - It escape *all* semi-effective (proof-checkable) theories.
> - it is not nameable or definable by the machine (as Gödel and Tarski saw).
>
> But that transcendental aspect, which is forced by logic, is available by
> the machine. So a universal machine can know that she is universal, and
> that makes her know that there is an unavoidable gap between its beliefs
> and truth, and that it can be used to explain why consciousness and
> knowledge seem so hard/impossible to define. In fact the theology of the
> machine introduces many nuance about that self: which correspond at
> different fields of research (p, the truth, []p, provability/believability,
> []p & p (knowledge, epistemology), []p & <>p (observability, as explained
> earlier or in my papers), and []p & <>t & p (sensibility, qualia).
>
> The unity here is given by a belief in Truth, the original main God of
> Plato/Parmenides/Plotinus. It is the truth we can search, and perhaps knows
> aspects on it, but never as such: doubt must remain for reason of
> self-consistency.
> With Mechanism, we can limit Truth to first order arithmetical truth, and
> all other notion (second order truth, analysis) can be put in the
> epistemology of the machine. Infinities only makes proof shorter.
>
> So, the unity of science is not a problem, if we come back to modesty in
> theology. The main formula from which all this can be derived is sometimes
> called the formula of modesty: []([]p -> p) -> []p (Löb formula), which is
> both akin to the view of the scientific attitude as essentially the
> doubting view (from Descartes to Popper) and to the religious attitude of
> ```

### Re: [Fis] Sustainability through multilevel research: The Lifel, Deep Society Build-A-Thon - 1

```Nikhil --  Leaving aside details of hierarchical structure, I point out,
concerning economics:

It seems that you have in mind a global economic system in your planning.
Is that so? I think that the current global capitalist system would need to
be eschewed.

Then, this also would seem to involve a world government, placing the types
of agriculture in their optimal regions, etc.

Alternative;y, perhaps your system might function on an island like
Australia?

STAN

On Thu, Dec 17, 2015 at 3:52 AM, Nikhil Joshi
wrote:

> Dear All,
> The research presented here is focused on gleaning insights leading to new
> solutions to the economics vs ecosystem conflict. The roots of many of
> our problems in ecological sustainability lie in the fact that our
> socio-economic systems are largely focused on fulfilling only human needs
> and the needs of human organizations. In doing so, as pointed out by Pedro,
> Bob, Francesco and others in this group our economics largely ignores the
> productive value of our ecosystems and the true costs of our development on
> our life supporting living systems.
>
> I term such a society as a “shallow society”, a society that is focused on
> the development of a single species and largely ignores the value of its
> own life-supporting living systems. With global population predicted to
> grow to 9 billion people, the next level of human development requires a
> transition of human society from being a “shallow society” that is only
> focused on only human needs to what I call a “deep society”. A deep
> society is a society that includes all living systems in its development.
>
> In this view, a deep society is not only focused on needs of human beings
> and their organizations but its development models also include development
> of the entire gamut of life-supporting living systems. Such a society
> grows not by exploiting the resources of a living planet, but also it
> possesses the capability to nurture, grow and actively manage a “living
> planet” (and perhaps seed life on other planets as well). Human
> development in the future will require the creation of new capabilities to
> develop models leading to a deep society. The question then is- can we
> develop systems that will enable a fair-value reciprocity and exchange
> between living ecosystems and economic systems?
>
>
> While, the notion that economics does not adequately value natural
> systems has been highlighted by many researchers in the field of ecological
> economics. Ideas on how natural systems can be understood, valued and
> integrated into economics have remained elusive. A multilevel view (like
> the one presented here) allows one to compare socio-economic
> organizations with natural organizations and could also provide new
> insights into how the dynamics of natural ecosystems could be synergised
> with economic systems.
>
> The model presented in the kick-off session shows two levels of
> energetically and materially coupled exchange networks in ecosystems. At
> the first level of exchange networks geochemical molecules are organized
> into different autotrophic species, and modulated by Mycorrhiza (level 1).
> Different autotrophic species then become food for the different
> heterotrophic species hence giving rise to the next higher level of
> exchange networks in ecosystems, modulated by gut bacterial networks (Level
> 2). The question then is- how does nature organize to build-in synergies
> between these two levels?
>
> At level 1, Mycorrhiza networks are known to modulate growth rates across
> different autotrophic species by providing phosphorous to different
> autotrophic species in quantitative exchange for carbohydrates. Autotrophic
> species (or groups of autotrophic species) that provide more carbohydrate
> hence get more phosphorous. Hence carbohydrates play a role in influencing
> phosphorous allocation across different autotrophic species connected to a
> Mycorrhiza network. At the next higher level in the exchange networks
> between different autotrophic species and different heterotrophic species
> gut bacteria use carbohydrates to modulate growth rates in heterotrophic
> species. Hence carbohydrates seem to play a role both in influencing
> dynamics in exchange networks at level 1, as well as in influencing
> dynamics in exchange networks at level 2.
>
> *Could such an organization where carbohydrates are a common influencing
> factor in exchanges at both levels serve to align both levels towards
> increasing overall carbohydrate production in ecosystems (hence increasing
> the overall primary production in ecosystems) by synergizing dynamics
> across both levels (and two different modulator networks)?*
>
> *Could this two-level role of carbohydrates provide new insights on
> aligning the third level of exchange networks (and our financial investment
> networks) with underling ecosystem exchange networks at level 1 and 2? *
> At this stage, these and other ideas ```

### Re: [Fis] Sustainability through multilevel research: The Lifel, Deep Society Build-A-Thon - 1

```Loet -- A metabiolgy does not imply that there would not be
more-than-biological properties and processes going on.  We would not
bother to identify a higher level unless it had some of its own emergent
properties.

STAN

On Fri, Dec 11, 2015 at 5:35 AM, Loet Leydesdorff
wrote:

> Dear colleagues,
>
>
>
> I don’t consider it as fruitful to recycle the argument that society were
> to be modeled as a meta-biology. The biological explanation can perhaps
> explain behavior of individuals and institutions; but social coordination
> more generally involves also the dynamics of expectations. These are much
> more abstract although conditioned by the historical layer. For example,
> one cannot expect to explain the *trias politica* or the rule of law
> biologically. These cultural constructs regulate our behavior from above,
> whereas the biological supports existence and living from below. The
> historical follows the axis of time, whereas the codification (albeit
> historical in the instantiations) also restructures and potentially
> intervenes and reorganizes social relations from the perspective of
> hindsight.
>
>
>
> In analogy to codifications such as the juridical ones, scientific
> knowledge provides the code for technological intervention. This type of
> knowledge is human-specific; perhaps, we are also able to build machines
> that mimick it. This technological evolution is going on for centuries. If
> I look up from my screen, I look into the gardens which have a typical
> Dutch polder vegetation. The polder was made in the 17th century and
> replaced the natural ecology of marsh land and lakes. The order of the
> explanation was thus inverted: the constructed structures (instead of the
> constructing agencies) increasingly carry the system. The constructs don’t
> have to be material; see my example of the rule of law. It is not a
> religion, but a dynamics of expectations. Replacing it with a biology
> misses the point.
>
>
>
> Best,
>
> Loet
>
>
> --
>
> Loet Leydesdorff
>
> Professor, University of Amsterdam
> Amsterdam School of Communication Research (ASCoR)
>
> l...@leydesdorff.net ; http://www.leydesdorff.net/
> Honorary Professor, SPRU, University of
> Sussex;
>
> Guest Professor Zhejiang Univ. ,
> Hangzhou; Visiting Professor, ISTIC,
> Beijing;
>
> Visiting Professor, Birkbeck , University of
> London;
>
>
>
>
> *From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Nikhil
> Joshi
> *Sent:* Friday, December 11, 2015 9:47 AM
> *To:* FIS Group
> *Cc:* Nikhil Joshi
> *Subject:* Re: [Fis] Sustainability through multilevel research: The
> Lifel, Deep Society Build-A-Thon - 1
>
>
>
> Dear Guy and FIS colleagues,
>
> the roots of biological systems and their evolution in dissipate systems
> are very interesting. Your paper reminds me of a paper by Virgo and Froese
> on how simple dissipative structures can demonstrate many of the
> characteristics associated with living systems, and the work of Jeremy
> England at MIT.
>
>
>
> Given your research focus and expertise in looking at living systems as
> dissipative systems, I would appreciate your views and assistance in
> understanding the energetics involved in the common multilevel
> organisational pattern (CMOP) (presented in the paper II of the kick-off
> mail).
>
>
>
> At first glance, it appears that different levels in self-organization in
> living systems  a core dynamic in living systems is comprised of a cycle
> between a class of more-stable species (coupled-composite species) and a
> class of less-stable species (decoupled-composite species), see paper II in
> the kick-off mail.
>
> hence:
>
> Level 1: Molecular self-organization, involves a cycle between oxidised
> molecules (more stable) and reduced molecules (less stable) in molecular
> self-organization in  photosynthesis and cellular metabolism [Morowitz and
> smith].
>
>
>
> Level 2: Cellular self-orgnaization, involves a cycle between autotrophic
> species (more stable) and heterotrophic species (less stable) in ecosystems
> [Stability of species types as defined by- Yodzis and Innes Yodzis, P.;
> Innes, S. Body Size and Consumer-Resource Dynamics. *Am. Nat.* 1992, *139*,
> 1151].
>
>
>
> Level 3: Social self-self-organization, involves a cycle between
> kinship-based social groups (more stable) and non-kinship-based social
> groups (less stable) [Stability of species types as suggested in Paper II,
> based on an extension of work of Robin Dunbar and others].
>
>
>
> At level 1 (molecular self-organiztion)- solar energy is stored in the
>  high-energy reduced molecules. Do you see a possibility that
> living systems could store energy in cycles involving less stable ```

### Re: [Fis] Locality & Five Momenta . . .

```Marcus wrote:

– I find myself thinking Five Momenta must represent five types of
localities. I ask if that “smells right” to you. If so, I would think that
“localizing hierarchies” would also be needed. For example, I see: 1)
passive descriptions of Nature (aka natural philosophy, general science) as
a different locality than, 2) anthropogenic or anthropocentric deeds (human
semiotics+acts). One might even then add 3) biological processes mediating
between 1 & 2.  All represent essentially different systems of meaning, no?
But then, the Five (suggested) Momenta would be subordinate to 1, 2, and 3
in different ways, as I read things. Evaluation (cataloguing) of different
localized traits seems to me as a possible useful path. Thoughts?

Marcus -- The momenta as given my Pedro:philosophy, biomolecular,
multicellular, sociality, information do not make up a logical hierarchy,
either subsumptive nor compositional. One possible, idealistic, reading is
in subsumption:

{mind {microbiology {macrobiology {sociality {conceptualization}

STAN

On Fri, Oct 30, 2015 at 2:49 AM, Marcus Abundis <55m...@gmail.com> wrote:

> Loet, thanks for your note (Sat Oct 24) . . . an interesting twist on
> things I had not been considering.
>
> John, re (Tue Oct 27) “rigorous connections using the entropy concept . .
> . most people don't understand entropy . . . So I haven't published”
> – This interests me, as my own work heads in a general “entropic”
> direction.
>
> Pedro, Steve & Stan – re various notes on Locality, Five Momenta and
> Hierarchy.
> – I find myself thinking Five Momenta must represent five types of
> localities. I ask if that “smells right” to you. If so, I would think that
> “localizing hierarchies” would also be needed. For example, I see: 1)
> passive descriptions of Nature (aka natural philosophy, general science) as
> a different locality than, 2) anthropogenic or anthropocentric deeds (human
> semiotics+acts). One might even then add 3) biological processes mediating
> between 1 & 2.  All represent essentially different systems of meaning, no?
> But then, the Five (suggested) Momenta would be subordinate to 1, 2, and 3
> in different ways, as I read things. Evaluation (cataloguing) of different
> localized traits seems to me as a possible useful path. Thoughts?
>
> Re Chatin – an interesting article, to be sure, but for the reasons Joesph
> points out (and more) I agree with his posted thoughts.
>
> Finally, in following the posted notes, I find this “discussion about
> discussion“ instructive.
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
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```

### [Fis] hierarchy

```Pedro wrote:

I see but five different and interrelated "momenta" that should be aligned
for the hypothetical advancement of the common info field.  The first one
corresponds to philosophy, as the critical playground where dissatisfaction
with the existing views should conduce to attempting more congenial new
ways of thinking. Unsolved problems of the sciences, when they are general
and affect several disciplines, easily generate philosophical debate--which
can be helpful to suggest new inroads. Saying clearly "nope" to some
philosophical and para-philosophical schools is quite valuable although it
easily generates irritation and obfuscation in the concerned parties (that
ingredient of "piquancy" also enlivens the debates).The second momentum
would correspond to the biomolecular (primordials of life and cellular
organization). The third momentum would wrap around the organismic and the
neuronal (the evolutionary outcomes of multicellular life up to advanced
nervous systems). I think they are so obvious that do not deserve further
comment.The fourth momentum involves the roots of human sociality, up to
the historical development of social complexity. And the fifth momentum
belongs to the contemporary revolution around communication, information,
etc.

Pedro -- What you have here is a rough subsumptive hierarchy.  That is,
each concept to the immediate left of another concept here subsumes that
concept.  So, e.g., sociality subsumes information, while information
constrains sociality.

{philosophy  {biomolecular  {organismic & neuronal  {sociality
{information}

STAN
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```

### [Fis] life cycles

```Pedro wrote:

Unfortunately, the neglect of the life cycle is almost universal. Neither
neuroscientists nor psychologists nor social scientists are sufficiently
aware of this invisible "water" that permeates all living stuff. Echoing
some old evolutionary statement, everything should made sense in relation
with the advancement of the corresponding life cycle. Just the superficial
observation of human exchanges in our societies, or in whatever historical
epoch, the conversational small-talk topics, the way people greet each
other, the gossip media... the condensates of the individuals' info cycles
are everywhere. A new conceptualization of information as accompanying the
development of human action for the sake of life cycles and subtending the
cooperation structures of economic life could have wide multidisciplinary
interest--I think. (Unfortunately, these adventures are discouraged: Mark
is terribly right about the sorrow state of our collective brain
reservoirs--poor universities! kingdoms of conventionalism and tunnel
vision).

Stan: One aspect of the life cycle is the rate of energy flow through a
system, which is well known in living systems, and appears to be similar in
all dissipative structures.  This is shown in this figure:

[image: Inline image 1]

Then we need to consider which life cycle we are going to investigate.  One
conversation? The duration of conference?, etc.

STAN
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```

### Re: [Fis] [Fwd: Re: Information is a linguistic description of structures]--T...

```Loet wrote:

I suggest to distinguish between three levels (following Weaver): A.
(Shannon-type) information processing ; B. meaning sharing using languages;
C. translations among coded communications.

So, here we have a subsumptive hierarchy"

{reduction of possibilities {interpretation {generalization}}}

STAN

On Thu, Oct 1, 2015 at 2:14 AM, Loet Leydesdorff
wrote:

> in other words, it's time we confess in science just how little we know
> about language, that we explore language's mysteries, and that we use our
> discoveries as a crowbar to pry open the secrets of this highly contextual,
> deeply relational, profoundly communicational cosmos.
>
>
>
> Dear colleagues,
>
>
>
> The vernacular is not sufficiently codified to contain the complexity of
> the sciences. One needs specialized languages (jargons) that are based on
> symbolic codification. The codes can be unpacked in elaborate language; but
> they remain under re-construction. The further differentiation of codes of
> communication drives the complexity and therefore the advancement of the
> sciences as discursive constructs.
>
>
>
> This cultural evolution remains rooted in and generated by the underlying
> levels. For example, individuals provide variety by making new knowledge
> claims. Since the selection is at the level of communication, however, this
> level tends to take over control. But not as an agent; it further
> differentiates into different forms of communication such as scientific
> discourse, political discourse, etc. Sociologists (Parsons, Luhmann) have
> proposed “symbolically generalized media of communication” which span
> horizons of meaning. “Energy”, for example, has a meaning in science very
> different from its meaning in political discourse. Translations remain of
> course possible; local organizations and agents have to integrate different
> meanings in action (variation; reproduction).
>
>
>
> In my recent paper on the Self-organization of meaning (at
> http://arxiv.org/abs/1507.05251 ), I suggest to distinguish between three
> levels (following Weaver): A. (Shannon-type) information processing ; B.
> meaning sharing using languages; C. translations among coded
> communications. The horizontal and vertical feedback and feedforward
> mechanisms (entropy generation vs. redundancy generation in terms of
> increasing the number of options) are further to be specified.
>
>
>
> Hopefully, this contributes to our discussion.
>
>
>
> Best,
>
> Loet
>
>
>
>
> --
>
> Loet Leydesdorff
>
> *Professor Emeritus,* University of Amsterdam
> Amsterdam School of Communication Research (ASCoR)
>
> l...@leydesdorff.net ; http://www.leydesdorff.net/
> Honorary Professor, SPRU, University of
> Sussex;
>
> Guest Professor Zhejiang Univ. ,
> Hangzhou; Visiting Professor, ISTIC,
> Beijing;
>
> Visiting Professor, Birkbeck , University of
> London;
>
>
>
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
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```

### Re: [Fis] Information and Locality Introduction

```Pedro wrote"

>Most attempts to enlarge informational thought and to extend it to life,
economies, societies, etc. continue to be but a reformulation of the former

S: Well, I have generalized the Shannon concept of information carrying
capacity under 'variety'...  {variety {information carrying capacity}}.
This allows the concept to operate quite generally in evolutionary and
ecological discourses.  Information, then, if you like, is what is left
after a reduction in variety, or after some system choice.  Consider dance:
we have all the possible conformations of the human body, out of which a
few are selected to provide information about the meaning of a dance.

STAN

STAN

On Fri, Sep 11, 2015 at 8:22 AM, Pedro C. Marijuan <
pcmarijuan.i...@aragon.es> wrote:

> Dear Steven and FIS colleagues,
>
> Many thanks for this opening text. What you are proposing about a pretty
> structured discussion looks a good idea, although it will have to
> confront the usually anarchic discussion style of FIS list! Two aspects
> of your initial text have caught my attention (apart from those videos
> you recommend that I will watch along the weekend).
>
> First about the concerns of a generation earlier (Shannon, Turing...)
> situating information in the intersection between physical science and
> engineering. The towering influence of this line of thought, both with
> positive and negative overtones, cannot be overestimated. Most attempts
> to enlarge informational thought and to extend it to life, economies,
> societies, etc. continue to be but a reformulation of the former ideas
> with little added value. See one of the last creatures: "Why Information
> Grows: The Evolution of Order, from Atoms to Economies" (2015), by Cesar
> Hidalgo (prof. at MIT).
>
> In my opinion, the extension of those classic ideas to life are very
> fertile from the technological point of view, from the "theory of
> molecular machines" for DNA-RNA-protein matching to genomic-proteomic
> and other omics'  "big data". But all that technobrilliance does not
> open per se new avenues in order to produce innovative thought about the
> information stuff of human societies. Alternatively we may think that
> the accelerated digitalization of our world and the cyborg-symbiosis of
> human information and computer information do not demand much brain
> teasing, as it is a matter that social evolution is superseding by itself.
>
> The point I have ocasionally raised in this list is whether all the new
> difference in the "way of being in the world" between life and inert
> matter (& mechanism & computation)---or not. In the recent compilation
> by Plamen and colleagues from the former INBIOSA initiative,  I have
> argued about that fundamental difference in the intertwining of
> communication/self-production, how signaling is strictly caught in the
> advancement of a life cycle  (see paper "How the living is in the
> world"). Life is based on an inusitate informational formula unknown in
> inert matter. And the very organization of life provides an original
> starting point to think anew about information --of course, not the only
> one.
>
> So, to conclude this "tangent", I find quite exciting the discussion we
> are starting now, say from the classical info positions onwards, in
> particularly to be compared in some future with another session (in
> preparation) with similar ambition but starting from say the
> phenomenology of the living. Struggling for a
> convergence/complementarity of outcomes would be a cavalier effort.
>
> All the best--Pedro
>
>
>
> Steven Ericsson-Zenith wrote:
>
>> ...The subject is one that has concerned me ever since I completed my PhD
>> in 1992. I came away from defending my thesis, essentially on large scale
>> parallel computation, with the strong intuition that I had disclosed much
>> more concerning the little that we know, than I had offered either a
>> theoretical or engineering solution.
>> For the curious, a digital copy of this thesis can be found among the
>> reports of CRI, MINES ParisTech, formerly ENSMP,
>> http://www.cri.ensmp.fr/classement/doc/A-232.pdf, it is also available
>> as a paper copy on Amazon.
>>
>> Like many that have been involved in microprocessor and instruction
>> set/language design, using mathematical methods, we share the physical
>> concerns of a generation earlier, people like John Von Neumann, Alan
>> Turing, and Claude Shannon. In other words, a close intersection between
>> physical science and machine engineering.
>>
>> ...I will then discuss some historical issues in particular referencing
>> Benjamin Peirce, Albert Einstein and Alan Turing. And finally discuss the
>> contemporary issues, as I see them, in biophysics, biology, and associated
>> disciplines, reaching into human and other social constructions, perhaps
>> touching on cosmology and the extended role of information theory in
```

### Re: [Fis] Fw: It-from-Bit and information interpretation of QM

```Terry, list --

Terry wrote:

We should not expect such a quip to be a sufficient explanation of
information in all its complexity. It is merely a useful mnemonic (coined
also by MacKay as a distinction that makes a difference) that captures
both Shannon's logic and Bateson's cybernetic implications. But this is not
all. If one wants to try to force this phrase to carry more of the weight
of completely characterizing information it should be further interpreted.
Notice that it is also an appropriate quip to describe the concept of
physical work— a gradient (or difference of potential) that is reduced in a
constrained way so that it generates an increase in a gradient or
difference in potential or pushes a system further from equilibrium.

S: We might also note that it stands for the existence of any material
objects, in that they are energy gradients temporarily differentiated from
the condition of equilibrium implied by the universal tendency to even out
all such gradients. These ‘make a difference’ from that ultimate condition.
The particular forms of such gradients are where the information is located
when any observer interacts with one.

STAN

On Mon, Jun 29, 2015 at 4:48 PM, Terrence W. DEACON dea...@berkeley.edu
wrote:

On Bateson's difference that makes a difference.

We should not expect such a quip to be a sufficient explanation of
information in all its complexity. It is merely a useful mnemonic (coined
also by MacKay as a distinction that makes a difference) that captures
both Shannon's logic and Bateson's cybernetic implications. But this is not
all. If one wants to try to force this phrase to carry more of the weight
of completely characterizing information it should be further interpreted.
Notice that it is also an appropriate quip to describe the concept of
physical work— a gradient (or difference of potential) that is reduced in a
constrained way so that it generates an increase in a gradient or
difference in potntial or pushes a system further from equilibrium.

This double applicability is not merely a terminological coincidence,
though I don't think that Gregory realized this, since he used this quip to
argue for an energy/information dichotomy. I have instead argued (most
recently in my January FIS essay) that both the referential and normative
properties of information are intimately entangled with the concept of
physical work.

Also, in English parlance the phrase to make a difference is an idiom
that means to matter or to be significant or of value. I believe that
this double entendre was intended in order to implicate the normative and
goal directed aspects of information. Explicating either the aboutness or
the normative consequence in terms of bits therefore inevitably results
in reductionistic oversimplication. Bits are a relevant measure of
intrinsic logical properties of the communication medium, but of minimal
value in assessing the extrinsic relational properties that are implicated
in the larger concept of information. I think that measuring work (though
in ways that are more complex than mere physical work) can lead to a more
useful incorporation of the referential and normative properties that are
implied by information.

Another problem is introduced by the use of the concept of meaning in
these discussions. The term ambiguously connotes both reference and
significance, and while it is applicable to symbolic and linguistic
information, it only metaphorically applies to iconic and indexical forms
of communication. Thus we discern that a sneeze indicates (provides
potential information about) an allergic response, but doesn't mean
allergy or nasal irritation. Seeing the imprint of a person's face on a
coin doesn't mean that person. I would not want to exclude these semiotic
forms of conveying information from our consideration of the concept.

Clearly, we need to carefully distinguish the intrinsic logical properties
of a signal medium (Shannon's usage) from information about something not
intrinsic to that medium, from the informative value or normative /
significant / useful consequence that is the point of interpreting
something to be about something else.

To fail to make these distinctions and instead flatten our discussions to
the Shannonian usage is to loose track of the challenge. Let me conclude by
noting that this troublesome flattening of the meaning of information was
recognized by Shannon and many others, in the formative years of the field.
In the words of a major figure in the field:

*“I didn’t like the term Information Theory. Claude didn’t like it either.
You see, the term ‘information theory’ suggests that it is a theory about
information – but it’s not. It’s the transmission of information, not
information. Lots of people just didn’t understand this... I coined the
term ‘mutual information’ to avoid such nonsense: making the point that
information is always about something. It is information ```

### Re: [Fis] Philosophy, Computing, and Information - apologies!

```Loet -- Well, so you favor the definition of information as an invention of
Western technology related to communication.  Others prefer to define
information in such a way that it emerges into the world with biology -- in
the genetic system.  Still others define information in such a way that it
can be viewed as a physical quantity, perhaps a measure of the importance
of context in any physical interaction.  As a generalizer, I prefer the
latter, giving us the subsumptive hierarchy:

Information ~ {context {material code {uncertainty}}}

STAN

On Sun, Jun 14, 2015 at 1:46 PM, Loet Leydesdorff l...@leydesdorff.net
wrote:

I would add another possibility -- information does not appear in the
universe until it is manipulated by modern human society as a commodity.

Yes, Stan, this makes sense to me: information (in bits) can be considered
as a measurement of the expected uncertainty. It is *yet* meaning-free,
but it can be provided with meaning in a system of reference – such as a
discourse.

For example, {50%,50%} contains 1 bit of information. Thus, if we mix 50
euro coins with 50 coins of a dollar or we group 50 black cats with 50
white ones, the uncertainty is one bit of information. This does not tell
us anything about the cats themselves as in a biology.

During the recent conference in Vienna, I was amazed how many of our
colleagues wish to ground information in physics. However, the
information-theoretical evaluation seems mathematical to me. The
mathematical notion of entropy is different from the physical one. The
physical one is only valid for the physico-chemical system of momenta and
energy.

When I exchange the 50 dollars into 50 euros, the expected information
content of the distribution of coins goes from one to zero bits, but this
is not thermodynamic entropy. The physics of the exchange process are
external to the informational-theoretical evaluation.

I know that you wish to express this with hierarchies. Information can be
measured at each level or as mutual information between them. But what the
information means, depends on the specific systems of reference.

Best,

Loet

--

Loet Leydesdorff

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

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

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

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

*From:* Fis [mailto:fis-boun...@listas.unizar.es] *On Behalf Of *Stanley
N Salthe
*Sent:* Sunday, June 14, 2015 3:14 PM

*To:* fis
*Subject:* Re: [Fis] Philosophy, Computing, and Information - apologies!

Krassimir -- Thanks. Now I see what your objection is.  You do not agree
with the Wheeler concept that information was he basis upon which
everything else was founded. Rather, you see it as appearing along with
matter. Or you might consider that it appeared 'along with form', in which
case information doesn't appear in the universe until life makes it
appearance.  I would add another possibility -- information does not appear
in the universe until it is manipulated by modern human society as a
commodity.

STAN

On Sat, Jun 13, 2015 at 3:49 PM, Krassimir Markov mar...@foibg.com
wrote:

Dear John and Stan,

What is cause, and what is result? This is the question.

If we not assume information and informational processes as secondary
effect from activity of living mater,  it is not possible to proof anything
and we have to believe that proposed models maybe are truth. We have to
trust to Author but not to experiments.

Information has to be included not in the beginning of the hierarchy – at
least in the middle where living mater appear.

Sorry that my post was apprehended as careless!

Friendly regards

Krassimir

*From:* Stanley N Salthe ssal...@binghamton.edu

*Sent:* Saturday, June 13, 2015 3:30 PM

*To:* Krassimir Markov mar...@foibg.com

*Subject:* Re: [Fis] Philosophy, Computing, and Information - apologies!

Krassimir -- ???  I fail to understand your assertion.  This (and any
hierarchy) is a logical formulation, allowing us to allocate influences
from various aspects of nature in an orderly manner.

STAN

On Fri, Jun 12, 2015 at 5:18 PM, Krassimir Markov mar...@foibg.com
wrote:

Dear John and Stan,

Your both hierarchies are good only if you believe in God.

But this is believe, not science.

Sorry, nothing personal!

Friendly regards

Krassimir

*From:* John Collier colli...@ukzn.ac.za

*Sent:* Friday, June 12, 2015 5:02 PM

*To:* Stanley N Salthe ssal...@binghamton.edu ; fis
fis```

### Re: [Fis] Philosophy, Computing, and Information - apologies!

```Pedro -- Your list:

physical, biological, social, and Informational

is implicitly a hierarchy -- in fact, a subsumptive hierarchy, with the
physical subsuming the biological and the biological subsuming the social.
But where should information appear?  Following Wheeler, we should have:

{informational {physicochemical {biological {social

STAN

On Fri, Jun 12, 2015 at 5:34 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Thanks, Ken. I think your previous message and this one are drawing sort
of the border-lines of the discussion. Achieving a comprehensive view on
the interrelationship between computation and information is an essential
matter. In my opinion, and following the Vienna discussions, whenever life
cycles are involved and meaningfully touched, there is info; while the
mere info circulation according to fixed rules and not impinging on any
life-cycle relevant aspect, may be taken as computation. The distinction
between both may help to consider more clearly the relationship between the
four great domains of sceince: physical, biological, social, and
Informational. If we adopt a pan-computationalist stance, the information
turn of societies, of bioinformation, neuroinformation, etc. merely reduces
to applying computer technologies. I think this would be a painful error,
repeating the big mistake of 60s-70s, when people band-wagon to developed
the sciences of the artificial and reduced the nascent info science to
library science. People like Alex Pentland (his social physics 2014) are
again taking the wrong way... Anyhow, it was nicer talking face to face as
we did in the past conference!

best ---Pedro

Ken Herold wrote:

FIS:

Sorry to have been too disruptive in my restarting discussion post--I did
not intend to substitute for the Information Science thread an alternative
way of philosophy or computing.  The references I listed are indicative of
some bad thinking as well as good ideas to reflect upon.  Our focus is
information and I would like to hear how you might believe the formal
relational scheme of Rosenbloom could be helpful?

Ken

--
Ken Herold
Director, Library Information Systems
Hamilton College
Clinton, NY 13323
315-859-4487
kher...@hamilton.edu mailto:kher...@hamilton.edu

--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta X
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 ( 6818)
pcmarijuan.i...@aragon.es
-

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### Re: [Fis] THE FOURTH GREAT DOMAIN OF SCIENCE: INFORMATIONAL? - What is a discipline?

```Bob-- As one who has strayed from the Darwinian discipline of evolutionary
biology (my erstwhile field), I can say that I have 'paid the price'. But I
have had a wonderful time exploring wherever my thinking has gone.  I think
the discipline has in a sense guided me anyway, as turning away from it was
part of my motivation.  That is the disciplines continue to exert their
effect in the reactions to them.

STAN

On Sat, May 23, 2015 at 9:24 AM, Bob Logan lo...@physics.utoronto.ca
wrote:

Dear Colleagues - I have been reading the posts in this thread and
enjoying the conversation. I started playing with the notion of discipline
and came up with these undisciplined playful thoughts which I believe
provide an interesting or at least an alternative perspective on the notion
of a discipline. A discipline is a tool, a way of organizing ideas that
result from scientific inquiry or any other form of scholarly activity and
even artistic activity. Now every tool provides both service and
disservice.  All of the posts so far have dealt with the service of
discipline. Here are some thoughts about the possible disservice of
discipline. Please take the following with a grain of salt. I believe the
notion of a  discipline is anti-thetical to scientific inquiry in the sense
that  it confines ones thinking to the confines of a discipline. One should
not be disciplined by a discipline but be free to go beyond the boundaries
of that discipline. Note that the root of the word discipline is disciple.
If one is to be free to explore new ideas and new phenomena one should not
be a disciple of the scientists or thinkers that created a discipline. Now
I am not saying that learning a discipline is a bad thing as it provides a
solid training and an understanding of how a set of principles describes
certain phenomena. It is a model of how a scientific, scholarly or artistic
practice can be carried out. As long as one does not become a disciple of
one's discipline or disciplines they can be very useful for creating a new
discipline or going beyond ones discipline. Perhaps the notion of
trans-disciplinary is not such a bad notion if one thinks of trans as
beyond.

As to the notion that there are these four super categories of disciplines
or great domains of science: Physics, biology, social and the 4th domain
which is computing or infomation depending on how one likes to classify
thing here are some thoughts. I find these classification schemes and their
inter-relations fascinating and useful. But I believe another challenge
worthy of consideration is to consider the interaction of the great domains
of science with the great domains of the humanities, ethics, the arts. How
does we connect the knowledge of the sciences with the wisdom of how to
best use that knowledge to benefit humankind. Here are some thoughts I
developed before this thread began that might be pertinent to our current
discussion. Science can be thought of as organized knowledge given that the
etymologically the word science derives from the Latin to know:
en.wiktionary.org/wiki/*science*
‎
. From Old French *science*, from Latin scientia (“knowledge”),
from sciens, the present participle stem of scire (“know”).

*Data, Information, Knowledge, Wisdom: *The relationship of data,
information, knowledge and wisdom

“Where is the wisdom we have lost in knowledge?

Where is the knowledge we have lost in information?” ­– TS Eliot

“Where is the meaning we have lost in information?” ­– RK Logan

“• Data are the pure and simple facts without any particular structure or
organization, the

basic atoms of information,

• Information is structured data, which adds meaning to the data and gives
it context and

significance,

• Knowledge is the ability to use information strategically to achieve
one's objectives, and

• Wisdom is the capacity to choose objectives consistent with one's values
and within a larger social context (Logan 2014).”
While checking out the etymology of science I encountered the following on
http://www.luminousgroup.net/2013/05/on-etymology-of-science.html

“This might be a good time to examine the etymology of the word *science*,
It comes from the Latin *scientia*, from *sciens*, which means *having
knowledge*, from the present participle of *scire*, meaning *to know*,
probably—and here's where it gets exciting—akin to the Sanskrit *Chyati*,
meaning* he cuts off*, and Latin *scindere*, *to split, cleave*.

Science operates by cutting off questions of value. And this is why I
advocate consideration of the four great domains of science with the great
domain of the humanities, the arts and ethics. The greatest challenges
facing humanity is not just increasing our store of knowledge through
science but also how we choose to deploy our scientific knowledge in the
best interest of human kind.

So ends my challenge to Moises Nisenbaum and Ken Herold with thanks for
stimulating this ```

### [Fis] Intelligence Science

```Stanley N Salthe wrote:

Pedro -- Here are my reactions :

Intelligence Science is a new science. It is the scientific spirit applied
to thought and mental processes and phenomena; it is an emergent
multidisciplinary direction of research. At the same time, it represents a
long-standing tradition in oriental thought. After the success of science
in grasping the rules of the natural world, and despite many false starts,
science has finally begun to focus on intelligence. Hence East and West
should meet here, Science and Art should meet here, and it is from here
that the new scientific paradigm and a new paradigm for civilization should
evolve.
In ancient times, human beings faced the challenges of existence. After a
long period of evolution, it is the time to go from a survival mode - how
to live better - and now face what A. Feln said: to think better is the
challenge to our integrity. “Know yourself” was the inscription in the
temple of Apollo. It can and should be taken to heart now more than in any
other age. Intelligence Science has been born at the right moment.

S: The “right moment” may be too late for our current cultures, which have
virtually destroyed the natural environment with its 'ecosystem services'!

Despite all their problems, all sciences are becoming richer and more
successful, above all technological disciplines. The Internet is the ‘roof’
over the Global Village in which this has taken place. Workers in the
work and also their feelings about their work. Intelligence Science emerges
naturally.

We need to continuously try to face and answer honestly the question: how
can the human factor be recognized and integrated naturally into science?
Science needs rethinking, humanity needs rethinking, the West and the East
need rethinking, so that we can benefit from the richness of human nature
and  bear the complexity of human thought. Integration is not easy, but we
must do it. If all civilizations develop, reach their limits and then fade,
contending among themselves, finally they must fail and destroy each other.
Alternatively, the Eastern and Western civilizations of today could
interact more dynamically observing, understanding and checking each other
to form a ‘new’ civilization that could go farther. Which alternative will
we choose? Intelligence Science burdens itself with this mission.

S: Civilization is mediated by language.  It seems that English has taken
precedence over all others as the current ‘lingua franca’.

From Artificial Intelligence (AI) to Intelligence Science (IS) is a
strategic transformation, a major contribution to science. Led by the
Chinese Association for Artificial Intelligence ( CAAI), Intelligence
Science was born in October, 2003. Since the first one created in Peking
University, in just the last decade, 27 universities have set up a
Department of Intelligence Science and Technology, and the number should
increase. We can say that IS has now created a new frontier of knowledge,
going from theory to practice and to education. But our task, the task of
this book, is to describe and participate in the research and development
of this still-forming frontier.

S: So it seems that Intelligence science’ will have a mechanistic basis.
That seems unnecessarily limiting!

Poincaré said: “if we can occasionally enjoy relative tranquility, it is
because of the tenacious struggle of our ancestors. If our vigor, our
vigilance relax a moment, we will lose the fruits that our ancestors gained
for us.
There is a poem of Master Hong Yi that can describe this new science: “I
come for the plant/ I leave the flower that has not bloomed yet,/it does
not mean this is not a fine scene,/waiting for later generations.” Due to
the interactive changes involving East and West I mentioned above, our
civilization has achieved a high degree of maturity in what is now a
precious wealthy and peaceful age.

S: I fail to see this as a “peaceful age”.

STAN
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### [Fis] Fwd: Beginnings and ends---Steps to a theory of reference significance

```-- Forwarded message --
From: Pedro C. Marijuan pcmarijuan.i...@aragon.es
Date: Mon, Jan 19, 2015 at 11:02 AM
Subject: Re: [Fis] Beginnings and ends---Steps to a theory of reference
significance
To: Stanley N Salthe ssal...@binghamton.edu

Good comment! But not only to me, it has general interest, you should put
it into the list too... ---Pedro

Stanley N Salthe wrote:

Pedro --  The Four Domains of Science diagram is reminiscent of the
hierarchy of scientific disciplines outlined by Comte, Spencer and Peirce.
Thus (using the subsumptive hierarchy):

{informational realm {physicochemical realm {Biological realm {social
realm

Information is here viewed as preceding any of the other realms.  It is
not clear how to understand this.  Peirce had in this position ‘Universal
Mind’, which I think could be viewed as informational. Comte had
mathematics here, reifying what many would take to be an emergent human, or
animal, capability.

Many today would likely not give information a separate realm, but would
take it to emerge with the physical world (?Wheeler?).  I think this
coincides with my own view.

STAN

On Sat, Jan 17, 2015 at 5:25 AM, pedro marijuan pcmarijuan.i...@aragon.es
mailto:pcmarijuan.i...@aragon.es wrote:

Thanks Stan (next Monday I will resend the figure). By the way, it
would be great if you can contribute to warm up the session!
Best--Pedro
BlackBerry de movistar, allí donde estés está tu oficin@

*From: * Stanley N Salthe ssal...@binghamton.edu
mailto:ssal...@binghamton.edu
*Date: *Fri, 16 Jan 2015 09:39:40 -0500
*To: *Pedro C. Marijuanpcmarijuan.i...@aragon.es
mailto:pcmarijuan.i...@aragon.es
*Subject: *Re: [Fis] Beginnings and ends---Steps to a theory of
reference  significance

Oedro -- The figure does not show in this message.

STAN

On Fri, Jan 16, 2015 at 6:43 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es mailto:pcmarijuan.i...@aragon.es wrote:

Dear Terry and FIS colleagues---and pirates,

Just a brief reflection on the below.

(From Terry's last message)...
So my goal in this case is quite modest, and yet perhaps also a bit
foolhardy. I want to suggest a simplest possible model system to
use
as the basis for formalizing the link between physical processes
and
semiotic processes. Perhaps someday after considerably elaborating
this analysis it could contribute to issues of the psychology of
human
interactions. I hope to recruit some interest into pursuing this
goal.

In my view, any research endeavor is also accompanied by some
ultimate goals or ends that go beyond the quite explicit
disciplinary ones. In this case, say, about the destiny of the
constructs that would surround the information concept (or the
possibility of framing an informational perspective, or a
renewed information science, or whatever), wouldn't it be
interesting discussing in extenso what could that ultimate
vision?

I mean, most of us may agree in quite many points related to
the microphysical ( thermodynamic) underpinning of
information, as it transpires in the exchanges we are
having--but where do we want to arrive finally with the
construction activity? I tend to disagree with localist aims,
even though at the time being they may look more prudent and
parsimonious. Putting it in brief, too briefly!, and borrowing
from Rosenbloom (P.S. 2013. On Computing: The Fourth Great
Scientific Domain) the idea is that information science,
properly developed and linked with computer science and
mathematics, should constitute one of the Great Domains of
contemporary science. The informational would go together with
the physical, the biological, and the social: constituting the
four great domains of science. See Figure below. Rather than
attempting the construction of another average or standard
discipline, information science is about the making out of one
of the “great scientific domains” of contemporary knowledge.

More cogent arguments could be elaborated on how to cover
sceintifically the whole information world (human societies,
behaving individuals, brain organization, cellular processes,
biomolecules) and the problem of interlocking--crisscrossing a
myriad of information flows at all levels. But the point is,
ends, although unassailable, may be as much important as
beginnings.

Thanks in advance for the patience!

---Pedro

**

*Figure 1. The Four Great Domains of Science*. The graphic
shows the network```

### Re: [Fis] MEPP

```Terry -- Replying

fast as possible given the bearing constraints. They are unconditional
maximizers. Life that has survived has been able to apply conditions upon
its entropy production, but that does not mean that it has enacted energy
conservation or energy efficiency policies.  Its mode is still maximizing,
but within limits.

Your phrases given the bearing constraints and within limits are the
critical issues to be focused on in my opinion [as I noted in my response
to Guy].

S: Yes.

T: But I do indeed argue that living processes can and do enact entropy
rate regulating mechanisms. This is of course an empirical question, and

S: Do you know the multiple papers by Adrian Bejan?  He has shown that in
all systems (he has tackled LARGE numbers of them, including the living),
using.  I think that this is exactly what MEPP would predict.

T: I have seen studies suggesting both results. My point is only that
autogenesis (which I use as a proxy for the simplest life-like dynamic)

S: Do you know these papers on autogenesis?  They were dissatisfied with
autopoiesis because it did not admit evolutionary change.

Csányi, V. and G. Kampis (1989).  Autogenesis: the evolution of replicative
systems. Journal of Theoretical Biology 114: 303-321.

Kampis, G., 1991. Self-modifying Systems in Biology and Cognitive Science:
A New  Framework for Dynamics, Information and Evolution. London: Pergamon
Press.

T: is a dissipative system that regulates the boundary constraints on its
rate of dissipation, and that this non-linearity is a critical
game-changer.

S: Regulates downward from physical maxima, but does not go below the
fastest non-damaging rates, therefore is ‘maximizing given constraints’,

T: In particular, for this discussion, I argue that this
constraint-ratcheting effect—where a distinctive dynamical configuration
can change the boundary constraints on its own constraint dissipation
tendency—

S: This is not clear.  Constraints are usually not thought of as
dissipatable.  Perhaps an example?

T: is what makes reference and significance possible. The resulting higher
order synergy constraint is neither a physical nor chemical constraint, but
a formal constraint.

S: By “formal” I Take it you mean organizational or structural.

T: Because of this it is thereby

S: ‘Could thereby be’ ?

substrate transferrable so that reference and significance are
maintainable despite complete replacement of physical substrates, i.e. via
reproduction.

S: Would an example be the use of yolk in embryos?

Without this property biological evolution is not possible.

S: Is the property in question the “formal” organization?

STAN

On Sat, Jan 10, 2015 at 3:42 AM, Terrence W. DEACON dea...@berkeley.edu
wrote:

Hi Stan,

as possible given the bearing constraints. They are unconditional
maximizers. Life that has survived has been able to apply conditions upon
its entropy production, but that does not mean that it has enacted energy
conservation or energy efficiency policies.  Its mode is still maximizing,
but within limits.

Terry:  Your phrases given the bearing constraints and within limits
are the critical issues to be focused on in my opinion [as I noted in my
response to Guy]. But I do indeed argue that living processes can and do
enact entropy rate regulating mechanisms. This is of course an empirical
question, and I have seen studies suggesting both results. My point is only
that autogenesis (which I use as a proxy for the simplest life-like
dynamic) is a dissipative system that regulates the boundary constraints on
its rate of dissipation, and that this non-linearity is a critical
game-changer.

In particular, for this discussion, I argue that this
constraint-ratcheting effect—where a distinctive dynamical configuration
can change the boundary constraints on its own constraint dissipation
tendency—is what makes reference and significance possible. The resulting
higher order synergy constraint is neither a physical nor chemical
constraint, but a formal constraint. Because of this it is thereby
substrate transferrable so that reference and significance are maintainable
despite complete replacement of physical substrates, i.e. via reproduction.
Without this property biological evolution is not possible.

— Terry

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### [Fis] MEPP

```TD: Autogenesis is also not a Maximum Entropy Production process because it
halts dissipation before its essential self-preserving constraints are
persistence depends.

possible given the bearing constraints. They are unconditional maximizers.
Life that has survived has been able to apply conditions upon its entropy
production, but that does not mean that it has enacted energy conservation
or energy efficiency policies.  Its mode is still maximizing, but within
limits.

GH: I think of [MEPP] as a thermodynamic version of natural selection in
which some alternative states are thermodynamically favored over others,
but this does not guarantee that dissipation will proceed to completion or
that the particular alternative that absolutely generates the most
efficient or effective dissipation will always be the manifested outcome
(if there are a number of similarly optimal paths available).  Contingency
on idiosyncratic configurations within and in the neighborhood of a system

S: I think that the keyword here is ‘striving’  Living things are mostly
always striving, so they reach for the maximum until it ‘hurts’.

GH: Would you argue that autogenesis is not an MEP process from this
somewhat fuzzy perspective?

TD:  This offers a challenge to a theory (MEPP) that has recently been
heralded as a key to explaining life. But it does not violate the basic
logic of far-from-equilibrium thermodynamics. It is  rather a further
development, that now includes a non-linear factor: dissipative processes
that collectively produce and modify their own boundary conditions. But as
with the introduction of an such nonlinearity this can produce some quite
unexpected emergent consequences. This is what makes the dynamic that we
call life so radically different in what it can do compared to non-living
dissipative dynamics.

This -snip- does suggest that we may need to modify claims that life is
merely an entropy maximizing process.

S: I think no one has argued that living systems are ‘merely’ entropy
production maximizers. That might be the view of the Universe, if it could
have a view. But finalities can be parsed as {entropy production {free
energy dissipation {work}}} on the template {physical process {chemical
actions {living activity}}}.  At each level we have finalities {Second Law
{Maupertuis’ least energy {goal seeking}}}. The outermost class is locally
the weakest impulse, but it acts continuously and ‘fills in’ immediately
there is any hesitation, while the innermost subclass is the most
immediately effective, but its enthusiasms come and go, and do not last.

STAN
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### Re: [Fis] Physical Informatics… (J.Brenner)

```Bob -- I think the viewpoint on information being expressed by Gerhard is
that which sees information to be embodied in configuration/conformation.
If a configured entity is in the world it necessarily will encounter other
configurations/conformations which will result in an 'interpretation' by
both parties.

STAN

On Mon, Oct 20, 2014 at 2:53 PM, Bob Logan lo...@physics.utoronto.ca
wrote:

Dear all - my take on this post is that the question of whether physical
processes are information is like the question: Is there a sound if a tree
falls in the forest and no one is there to listen? This is like the Zen
koan: what is the sound of one hand clapping If no one is in the forest
are the trees information? Well for sure they are trees but as to whether
or not they are information that is strictly dependent on the point of view
of the respondent. For me they are just trees and here is why I think so.
For me information is about a process. The noun information relates to the
verb inform. If no one is being informed there is no information. In the
same way that if no one or thing is there being loved (verb) their is no
love (noun). If no one is engaged in the activity of loving (a verb) there
is no love (a noun). If there is no one being informed (a verb) then there
is no information (a noun). Now one can talk about an object or a
phenomenon having the possibility of informing someone which to my mind is
potential information which is what I would call the physical processes
that take place in our universe. A book written in Urdu is potential
information because an Urdu reader can be informed by it. For me as a
non-Urdu speaker there is very little information other than someone went
to the trouble of writing out a text with Urdu letters and hence there is
probably information there for an Urdu speaker reasoning why would any one
make the effort to create such an object unless that person wanted to
inform Urdu speakers. Just as one person's food is another person's poison
so it is that one person's information is just for another persons merely a
physical phenomenon such as processes in nature, ink on paper, sounds or EM
signals. Shannon developed a theory of signals in which some of those
signals have the ability to inform some recipients. I hope this collection
of words has informed you other than giving you the knowledge of my view as
to what constitutes information. Thanks to Joseph, Pedro, and Igor for the
opportunity to reflect on the nature of information. If you enjoyed my post
an email off line and I will send you an email version of my book *What
is Information?  Propagating Organization in the Biosphere, the
you know what an infomercial is. This was an infomercial because of my
offer to share my book with you erudite scholars of FIS whose posts I
always enjoy. With kind regards - Bob
__

Robert K. Logan
Prof. Emeritus - Physics - U. of Toronto
Chief Scientist - sLab at OCAD
www.physics.utoronto.ca/Members/logan
www.researchgate.net/profile/Robert_Logan5/publications

On 2014-10-20, at 1:57 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ wrote:

- Original Message -
*From:* Joseph Brenner joe.bren...@bluewin.ch
*To:* Igor Gurevich iggurev...@gmail.com ; Pedro C. Marijuan
pcmarijuan.i...@aragon.es ; fis fis@listas.unizar.es
*Sent:* Monday, October 20, 2014 8:40 AM
*Subject:* Re: [Fis] Physical Informatics contains fundamental results
which impossible to get only by physical methods

Dear Igor, Dear Gerhard and Colleagues,

In Igor's summary of his recent work, I read the following absoutely
critical statement:
It is shown that the expansion of the Universe is the source of
information formation, wherein a variety of physical processes in an
expanding Universe provide information formation. I take this as meaning
that the expansion of the Universe as such does not produce information.

Gerhard's formulation is slightly different (my paraphrase):
The first assymetry in energy distribution, following the singularity, is
the source of information formation.

My question is, therefore, how best to combine these insights. For
example, we may say that the variety of physical processes are all the
consequence of, and subsequently reflect, a first assymetry.

It is also interesting to note that the approaches of both Igor and
Gerhard imply the emergence of information through the interactional impact
(informational interactions) of fundamental forces on particles, extended
by Gerhard to somewhat higher levels of organization (life) than Igor.

I look forward to further discussion of these fundamental issues.

Sincerely,

Joseph

- Original Message -
*From:* Igor Gurevich iggurev...@gmail.com
*To:* Pedro C. Marijuan ```

### Re: [Fis] Fw: Krassimir's Information Quadruple and GIT. Quintuples?

```Bob wrote:

Recall that some thermodynamic variables, especially work functions like
Helmholz  Gibbs free energies and exergy all are tightly related to
information measures. In statistical mechanical analogs, for example, the
exergy becomes RT times the mutual information among the molecules

S: So, the more organized, the more potential available energy.

I happen to be a radical who feels that the term energy is a construct
with little ontological depth.

It is a bookkeeping device (a nice one, of course, but bookkeeping
nonetheless).
It was devised to maintain the Platonic worldview. Messrs. Meyer  Joule
simply
gave us the conversion factors to make it look like energy is constant.

S: It IS constant in the adiabatic boxes used to measure it.

*Real* energy is always in decline -- witness what happens to the work
functions I
just mentioned.

S: In decline in the actual material world that we inhabit.  That is, the
local world -- the world of input and dissipation.  I think the information
problem may be advanced if we try to explain why the energy efficiency of
any work is so poor, and gets worse the harder we work. This is the key
local phenomenon that needs to be understood.

STAN

On Mon, Aug 25, 2014 at 4:40 AM, John Collier colli...@ukzn.ac.za wrote:

Nice post, Bob. I agree pretty much. Brooks and Wiley got slammed by
Morowitz for using the *Real* energy in their book, which being about
biology is the only sensible notion of energy.

There is still a need for a clear dimensional analysis of the relation(s)
between information and energy. I work on that periodically, but only
minimal progress so far. Perhaps I can focus on it better now that I am
retired.

John

At 02:11 AM 2014-08-22, Robert E. Ulanowicz wrote:

Dear Joseph,

Recall that some thermodynamic variables, especially work functions like
Helmholz  Gibbs free energies and exergy all are tightly related to
information measures. In statistical mechanical analogs, for example, the
exergy becomes RT times the mutual information among the molecules.

I happen to be a radical who feels that the term energy is a construct
with little ontological depth. It is a bookkeeping device (a nice one, of
course, but bookkeeping nonetheless). It was devised to maintain the
Platonic worldview. Messrs. Meyer  Joule simply gave us the conversion
factors to make it look like energy is constant. *Real* energy is always
in decline -- witness what happens to the work functions I just mentioned.

Well, enough heresy for one night!

Cheers,
Bob U.

Dear Mark and All,

I return belatedly to this short but key note of Mark's in which he
repeats his view, with which I agree, that  Energy is a kind of
information and information is a kind of energy.

My suggestion is that it may be useful to expand this statement by
looking
at both Information and Energy (mass-energy) as emergent properties of
the
universe. Since we agree they are not identical, we may then look at how
the properties differ. Perhaps we can say that Energy is an extensive
property, measured primarily by quantity, and Information is an
intensive
property. The difficulty is that both Energy and Information themselves
appear to have both intensive and extensive properties, measured by
vector
and scalar quantities respectively. I am encouraged to say that this
approach might yield results that are compatible with advanced theories
based on the sophisticated mathematics to which Mark refers.

I would say then that in our world it is not the question of which is
more
fundamental that is essential, but that Energy and Information share
properties which are linked dynamically. In this dialectical
interpretation, the need for a 'demon' that accomplishes some function,
as
in the paper referred to in John's note, is a formal exercise.

Thank you and best wishes,

Joseph

- Original Message -
From: Burgin, Mark
To: Joseph Brenner
Sent: Friday, August 01, 2014 9:19 PM
Subject: Re: [Fis] Krassimir's Information Quadruple and GIT.
Quintuples?

Dear Joseph and Colleagues,
An answer to the perhaps badly posed question of whether information or
energy is more fundamental is given in the book M.Burgin, Theory of
information. The answer is a little bit unexpected:
Energy is a kind of information and information is a kind of energy.
It's a pity that very few researchers read books with advanced theories
based on sophisticated mathematics.

Sincerely,
Mark Burgin

On 7/31/2014 2:40 AM, Joseph Brenner wrote:

Dear Krassimir and Colleagues,

I have followed this discussion with interest but not total agreement.
As I have commented to Krassimir previously, I feel that his system,
based on symbols as outlined in his paper, is too static to capture the
dynamics of complex information processes and their value (valence). It
suffers ```

### Re: [Fis] information.energy

```Bob -- Note that I was pointing out a sense in which information implies
something different from energy -- especially in the context of dialectics,
which is the basis of Joseph's approach. There can be no 'precipitated'
energy (matter) without some kind of form, realizing one or some
constraints, but the concept of information (its history) tends to imply
interaction.

STAN

On Sun, Aug 3, 2014 at 11:13 PM, Robert E. Ulanowicz u...@umces.edu wrote:

Stanley N Salthe ssal...@binghamton.edu
9:32 AM (0 minutes ago)
to Joseph
Joseph -- Commenting on:
...
Is there not also a sense that information implies more than one entity
(sender-receiver, object-interpreter)? That too would tend to align with
the idea of energy being primary.

But Stan, you were one of the first to recognize the broader nature of
information as constraint. It is also inherent in structure (Collier's
enformation). Hence, wherever inhomogeneities exist, so does information
-- an argument for a common origin. Bob

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### [Fis] information.energy

```Stanley N Salthe ssal...@binghamton.edu
9:32 AM (0 minutes ago)
to Joseph
Joseph -- Commenting on:

We may agree that, if they are not identical, energy and information
always accompany one another and may have emerged together from some as yet
incompletely defined substrate. However, they may not be, do not have to be
and for me are not at the same ontological level, and energy is primary
being less abstract.

Is there not also a sense that information implies more than one entity
(sender-receiver, object-interpreter)? That too would tend to align with
the idea of energy being primary.

STAN
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### Re: [Fis] [Fwd: closing the session] John Prpic

```With hierarchy theory serving as a dressmaker's dummy, these statements:

From Guy:
*I think of collective intelligence as synonymous with collective
information processing*. I would not test for its existence by asking if
group-level action is smart or adaptive, nor do I think it is relevant to
ask whether collective intelligence informed or misinformed individuals.  I
would say that in the classic example of eusocial insect colonies (like
honey bees, for example) *there is no reasonable doubt that information is
processed at the level of the full colony, which can be detected by the
coordination of individual activities into coherent colony-level
behavior*. *Synchronization
and complementarity of individual actions reflect the top-down influences
of colony-level information processing.* It is the existential question
that I think is key here, and I hope our conversation includes objective
ways to detect the existence or absence of instances where a collective
intelligence has manifested as a way to keep this concept more tangible and
less metaphorical.

From John Collier:
Guy, This looks fruitful, but it might be argued that the exchanges
of information
in a colony can be reduced to individual exchanges and interactions, and
thus there is not really any activity that is holistic. This is what Steven
is doing with his example of pyramid building. *On the other hand, with
ants, for example, it has been shown by de Neuberg and others that in ant
colonies the interactions cannot be reduced, but produce complex
organization that only makes sense at a higher level of **behaviour.* Examples
are nest building and bridge building, among others. I assume the same is
true for humans. For example, in the pyramid case, why is it being built,
why are people so motivated to cooperate on such a ridiculous project?
Contrary to widespread opinion the workers were not slaves, but they were
individual people.* I doubt this can be explained at the individual level.
If ants have complexly** organized behaviour, then surely humans do as well
-- we are far more complex, and our social interactions are far more
complex*.

seem to be the most interesting garment designs!

STAN

On Mon, Apr 28, 2014 at 4:19 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Original Message   Subject: Re: closing the session  Date:
Sun, 27 Apr 2014 16:30:44 -0700  From: John Prpic
pr...@sfu.capr...@sfu.ca  To:
Pedro C. Marijuan pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es

Dear FIS'ers,

In an effort to put the latest session formally to bed, please allow me to
highlight some of the excellent food for thought that was put forward by
the group in respect to Collective Intelligence. I'll attempt to roughly
within this, I'll highlight passages that I thought were especially
interesting, salient, insightful or provocative.

From Pedro:
*Along the biggest social transformations, the new information orders
have been generated precisely by new ways to circulate
knowledge/information across social agents*--often kept away from the
previous informational order established. But there is a difference, in my
opinion, in the topic addressed by John P., it is *the intriguing, more
direct involvement of software beyond the rather passive, underground role
it generally plays*.  Organizational processes frozen into the
artifact--though not fossilized. Information Technologies are producing an
amazing mix of new practices and new networkings that generate growing
impacts in economic activities, and in the capability to create new
solutions and innovations...Brave New World? Not yet, but who knows...

From Bob Logan:
*What is a culture after all but a form of collective intelligence.*Eric
Havelock called myths the tribal encyclopedia. With writing the
collectivity of intelligence grew wider as evidenced by the scholars of
Ancient Greeks who created a collective intelligence through their writing.
The printing press was the next ramping up of collective intelligence as
the circle of intelligences contributing to a particular project
dramatically increased. The ability to have a reliable way of storing and
sharing experimental data contributed in no small way to the scientific
revolution. Other fields of study thrived as a result of print IT such as
philosophy, literature, history, economics etc etc. The printing press also
contributed to the emergence of modern democracy. *With the coming of
electricity and electrically configured IT the collectivity of intelligence
passed through another phase transition*. Marshall McLuhan reflecting on
this development well before the emergence of digital IT wrote:

The university and school of the future must be a means of total
community participation, not in the consumption of available knowledge, but
in the creation of completely unavailable insights. The overwhelming
obstacle ```

### [Fis] replies to Loet Joseph

```Replying to Loet and Joseph:

Loet:  I am not sure that you mean this with actuality. (which seems an
Aristotelian notion to me).

S: I have been using 'Actuality' (and 'Reality') as proposed by:

Roth G, Schwegler H (1990) Self-organization, emergent properties and the
study of the world.  In Krohn W, Kuppers G, Nowontny H (eds)
Self-Organization: Portrait of a Scientific Revolution. Kluwer.

Joseph: The first thing I would like, Stan, is that in your talking about
MY notion of actuality, it is brought out that it is no longer the original
concept elaborated by Aristotle, but that the (partial) actuality of the
elements involved in a dynamic process is linked dynamically to their
(partial) potentiality and *vice versa*.

S: I include potentiality as part of Actuality. Actuality exists at many
scales, and what is potential at, say, a large scale may be accompanied by
actions already actualized at a smaller scales. Thus, if it takes one
minute to complete an action at one scale (as viewed by an outside
observer), and simultaneously an action is being made at a smaller scale
that takes one second to complete, when that action is seen to be completed
at the smaller scale, the larger scale action (as viewed by the outside
observer) would still be happening/unfinished. Of course, there are no
outside observers, but actions at all levels will depend in various upon
what is happening at other levels.

Then Stan, I hope you could reconsider your formulations, with none of
which I can agree:

1. You set up a *distinguo* between reality and actuality, while failing to
see that both Loet and I are indeed concerned with both. Speaking for
myself, you should already see that I cannot have ignored the difference
between actuality and reality since I say that reality is composed of
actuality and potentiality. It is not a model of anything.

S: I'm sorry to disagree. Your dialectical system is a logical social
construct, and therefore a part of Realty (as per my take on Roth
Schwegler). Your system indeed* refers to* what I call 'Actuality' as an
element in the theory (this Actuality is again a social construct).

LIR is a part of reality, as is any logical, scientific theory but then
what is the purpose of saying It is a socially constructed tool for
negotiating actuality. Is your work a 'socially constructed tool'?

S: Yes indeed, it is.  Our thinking is located within Western discourse,
which is currently located within our capitalist system, and reflects
concepts that are possible/feasible within that system -- even if the
concepts are critical of it. You may contact some aspects of actuality with
your tongue or foot, but not with a theory (as such).  (These contacts
would be biological constructs, by the way, and no more privileged than
social constructs!).

Finally, as we all struggle to understand one another, what, Stan, is the
purport of the word 'negotiating' actuality? Negotiating for me means
seeking advantage of some kind, more or less (usually less) fairly. There
is a vicious ad for a financial broker you may have heard, which I cannot
stand: Life is a competition; negotiate well.

S: 'Negotiating', as I use it here, refers to trying to do one's best to
survive or succeed, involving also the use of versions of reality in order
to do so. The import is that actuality is a challenging experience.

(Your quote is indeed crass, and reflects the high status of Darwinian
notions in our culture.  I have a Critique of the Concept of Natural
Selection in my web pages at http://www.nbi.dk/~natphil/salthe/index.html )

STAN
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### Re: [Fis] Social constructivism

```In my last posting for the week, I Reply to Hans --

QBism does not change any of the impressive successes of quantum mechanics.
It simply says that quantum mechanics is a very complex, abstract encoding
of the experiences of generations of scientists interacting with atomic
systems.

S: These generations of “scientists” are a subsystem of society as a
whole.  They influence each other via language and other social
constructions, including theories and machines.  Through them, it is
society that observes the micro activities occurring with the experimental
machinery.  ‘Proof’? -- each individual could be replaced by another using
the same social tools (including education).

It disenfranchises a physicist from knowing what an electron spin, for
example, REALLY is, while celebrating her ability to predict correctly,
albeit probabilistically, what to expect in the next experiment. She and
her predecessors have created an abstract model, and validated it by appeal
to experiments, without appeal to any of the other considerations listed
above

S: So QM, via QBism, is meaningless!  Is this an achievement? -- to render
meaningless the activities within the socially-constructed machinery guided
by the socially-constructed theories?

In conversation with Joseph Brenner and others I have used the rainbow as a
metaphor. The rainbow is a phenomenon that everyone experiences slightly
differently, but that we all agree on.

S: I would say that it is a biologically-constructed epiphenomenon.

The scientific model that explains it is very complicated and highly
abstract.  Is the rainbow real?  It certainly does not exist when nobody
is looking.  It is, in the end, a personal experience.  For me the
experience is enhanced considerably by my understanding of the scientific
model of it, because it allows me to look for and discover details I had
never noticed, but I would not presume to say I know what YOUR experience
of it is.  Maybe you are thinking of Iris or Noah, and feeling awe or
curiosity, and remarking on its (apparently) immense size and variable
brightness.

S: But it’s physical interpretation, from the QBist perspective, is of no
interest as such.

QBism suggests that we look at the world as consisting of rainbows -- an
ensemble of complex phenomena about which we know some things, but whose
essences we cannot capture.  The QBist says: I don't know what the world
is.  All I know is what I experience in my interactions with the world, as
they are illuminated and modified by what I have learned from other people,

past and present, who have had similar experiences and encoded them in the
succinct language of mathematics.

S: That is, our experiences are socially conditioned biological
constructs.  In this view physics becomes the theoretical basis for
constructing the QM machinery, which will display an epiphenomenon.

STAN

Hans

On Tue, Jan 7, 2014 at 6:52 PM, Hans von Baeyer henrikrit...@gmail.comwrote:

Stan asks: Would we be justified in viewing QBism the latest venture of
[social] constructivism?

WOW, I sure hope not!  While it is true that there are fads in science,
and that the direction of research is influenced to some degree by the
society that funds it and consumes its fruits, I think that the underlying
methodology distinguishes socially constructed models of reality from
scientific ones.  Social constructions use arguments that play no role in
any account of the scientific method as it applies to the Natural Sciences
(as opposed to the Social Sciences).

Some examples: Deutsche Physik referred to the ethnicity of scientists,
Lysenkoism adduced ideological goals; Creationism appeals to scripture;
Feminist Science Studies consider the gender of scientists.

QBism does not change any of the impressive successes of quantum
mechanics.  It simply says that quantum mechanics is a very complex,
abstract encoding of the experiences of generations of scientists
interacting with atomic systems. It disenfranchises a physicist from
knowing what an electron spin, for example, REALLY is, while celebrating
her ability to predict correctly, albeit probabilistically, what to expect
in the next experiment. She and her predecessors have created an abstract
model, and validated it by appeal to experiments, without appeal to any of
the other considerations listed above.

In conversation with Joseph Brenner and others I have used the rainbow as
a metaphor. The rainbow is a phenomenon that everyone experiences slightly
differently, but that we all agree on. The scientific model that explains
it is very complicated and highly abstract.  Is the rainbow real?  It
certainly does not exist when nobody is looking.  It is, in the end, a
personal experience.  For me the experience is enhanced considerably by my
understanding of the scientific model of it, because it allows me to look
for and discover details I had never noticed, but I would not presume to
say I know what YOUR ```

### [Fis] QBism

```Here I advance a viewpoint for Hans.  There has been an ongoing critique of
the very scientific viewpoint that you eschew -- namely the notion that
there is an objective world out there that we might discover.  This attack
on science as it has been is known as social constructivism, and it is
sorely hated by most scientists, (Social constructivism has other meanings
in other fields, like architecture, but I refer only to its meaning
bis-a-vis science.) It proposes that observations are taken from local
perspectives -- as you do -- but it focuses ,not upon individual
researchers, as you do -- but rather upon the society from within which the
observations are made. Thus, modern science is taken to be an aspect, or
arm, of the Global Capitalist Growth Economy, which pays for the scientific
tools and work.  Hence, scientists are not viewed as discovering things,
but as constructing them, using the tools provided by society.  So, how do
you relate QBism to social constructivism?  Would we be justified in
viewing QBism the latest venture of constructivism?

STAN
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### Re: [Fis] reply to Loet

```Joseph said:

Of course it is persons, and not systems, in their complexity, that are
communicating and not communicating and wondering whether to continue to
communicate or not, or are sorry they communicated. Any attempt at a more
complete understanding of communication should be able to take such
complexification of the notion of system into account, in my opinion.

S: Here, in my thinking, you are broaching the internalist / externalist
dichotomy.   Hierarchy, as I have just outlined it in a recent posting, is
a global systems model -- an externalist construction such as is used in
the natural sciences.  When you refer to a human person, you are referring
to an entirely different order of entity.  Persons peer out at the universe
from their local positions -- from inside themselves. They have no place --
as unique persons -- in systems diagrams or models like the hierarchy
models.

Bruno said:

This thread reminds me George Bush when he said that that corporations are
persons.

S: It was the Supreme Court -- many appointed by Butch -- that said that.
In any case, you can see from my comments above that this statement is
sheer nonsense.  Corporations are subsystems of a Corporative State (phrase
coined by Mussolini).  They are unable to vote, as such, but they can
deploy costly messages aimed at defeating politicians who are not striving
to increase their corporate power.

STAN

On Sat, Nov 2, 2013 at 12:40 PM, Joseph Brenner joe.bren...@bluewin.chwrote:

Dear Gordana and Loet,

I think that you here and Loet, with his idea of local inversion of the
hierarchy, have an intuition of something I consider potentially very
important. In reality, it is the processes in the hierarchy that
have been moving and continue to move partly in a non-univocal manner,
countercurrently if you like. My logic gives a framework for such
movement in a spiral, not circular manner by alternating actualization and
potentialization.

Of course it is persons, and not systems, in their complexity, that are
communicating and not communicating and wondering whether to continue to
communicate or not, or are sorry they communicated. Any attempt at a more
complete understanding of communication should be able to take such
complexification of the notion of system into account, in my opinion.

Best,

Joseph

- Original Message -
*From:* Gordana Dodig-Crnkovic gordana.dodig-crnko...@mdh.se
*To:* Loet Leydesdorff l...@leydesdorff.net ; 'Stanley N
Salthe'ssal...@binghamton.edu;
'fis' fis@listas.unizar.es
*Cc:* Инга inga@mail.ru
*Sent:* Saturday, November 02, 2013 9:51 AM
*Subject:* Re: [Fis] reply to Loet

Could it possibly be imagined as a circular motion (bottom-up--top-down—
and-back-again)?

Just a thought.

All the best,

Gordana

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

From: Loet Leydesdorff l...@leydesdorff.net
Date: Saturday, November 2, 2013 8:21 AM
To: 'Stanley N Salthe' ssal...@binghamton.edu, 'fis'
fis@listas.unizar.es
Cc: Инга inga@mail.ru

Subject: Re: [Fis] reply to Loet

S: (Nothing can go against the 'entropy law'.)  A nice example for you
might be communication over distances by flashing lights using the Morse
code.  The actual local operations here may not be the best framework to
view this (including in thermodynamic terms). Again, I could subsume this
example into my above argument -- that is, it is the social system that is
communicating, not individual persons.  It takes two positions for this
communication to occur, and this makes the system a large scale one, and so
its speed of communication is understandable in terms of natural hierarchy
principles.

I don’t follow the argument completely: the larger social system would
then be subsumed under the individual system (because of its larger size
and speed), but it is a social construction on top of the individuals,
isn’t it? Is there room for a local inversion of the hierarchy (and thus of
the second law?) such as the generation of redundancy?

Best,

Loet

!--[if !supportLists]--・!--[endif]--Inga Ivanova and Loet
Leydesdorff, Redundancy Generation in University-Industry-Government
Relations: The Triple Helix Modeled, Measured, and
Simulated.http://arxiv.org/abs/1308.3836

!--[if !supportLists]--・!--[endif]--Loet Leydesdorff and
Inga Ivanova, Mutual Redundancies in Inter-human Communication Systems:
Steps Towards a Calculus of Processing
Meaninghttp://arxiv.org/abs/1301.6849,
*Journal of the American Society for Information Science and Technology *(in
press).

--

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### Re: [Fis] reply to Loet

```As my last posting for the week ...

Loet, Gordana --

Loet Leydesdorff
3:21 AM (6 hours ago)
to *Инга*, me, fis

S: (Nothing can go against the 'entropy law'.)  A nice example for you
might be communication over distances by flashing lights using the Morse
code.  The actual local operations here may not be the best framework to
view this (including in thermodynamic terms). Again, I could subsume this
example into my above argument -- that is, it is the social system that is
communicating, not individual persons.  It takes two positions for this
communication to occur, and this makes the system a large scale one, and so
its speed of communication is understandable in terms of natural hierarchy
principles.

L: I don't follow the argument completely: the larger social system would
then be subsumed under the individual system (because of its larger size
and speed), but it is a social construction on top of the individuals,
isn't it? Is there room for a local inversion of the hierarchy (and thus of
the second law?) such as the generation of redundancy?

SS: Ah, we have here opened a difficult and intriguing question.  First, a
non-social animal -- say, a leopard -- is an individual utilizing its
species' genetic potenialities.  These are contained within it, and its
acts as its species' representative -- but it acts alone, as a single
organism.

But a social animal is not alone, cannot act naturally alone.  It is a
portion of a larger group.  It is not an individual organism except when it
dies. Then we transit to a human social individual within his/her
socially-constructed frameworks. Even calling to another person in the
street is a group action (via language and expectations).  More clearly, if
the individual (as we think of ourselves) sends an e-mail message --  this
action is NOT an individual, personal action. It is the social system
acting through one of its parts.   The message itself is socially
constructed, as is the thought behind it.

Hierarchically (the compositional hierarchy is relevant here), the social
system is of much larger scale than its organismic parts.  One of these
cannot call by voice beyond the distance of two streets.  But the social
system can send messages at comparatively great speed (more power), and so
to greater distances.  As a social being, I can void waste alone, but I can
do hardly anything else by myself.  Even my language is an aspect of the
society, and so also any possible message I might make using it (otherwise
I would be judged insane!).

So -- no, the social system is not subsumed within the individual, but,
instead,  as the larger scale entity, occupies the individual, guiding
his/her actions. Even terrorists act within systemic guidelines, utilizing
a system's powerful products, guided by allowable alternative entrainment.

Thus, Gordana, bottom-up, yes.  Also top-down!  Bottom-up supplies and
generates possibilities, top-down regulates the deployment of these in
various constructions.

Concerning the Second Law of thermodynamics (a social construct!), it can
be viewed as imposing a finality upon our actions. Along with other
finalities -- (utilizin the subsumptive hierarchy) on the template of:

{physical world {material world {biological world {socioeconomic world

We have:

{entropy production {free energy dispersion {work {projects

The requirement for entropy production is weak compared to entrainment by
social projects, but it acts continually, in anything anyone does, by way
of the constitutively poor energy efficiency of any and all effective work.
Consequently, as we build, we serve the expanding universe even more!

STAN

On Sat, Nov 2, 2013 at 3:21 AM, Loet Leydesdorff l...@leydesdorff.netwrote:

S: (Nothing can go against the 'entropy law'.)  A nice example for you
might be communication over distances by flashing lights using the Morse
code.  The actual local operations here may not be the best framework to
view this (including in thermodynamic terms). Again, I could subsume this
example into my above argument -- that is, it is the social system that is
communicating, not individual persons.  It takes two positions for this
communication to occur, and this makes the system a large scale one, and so
its speed of communication is understandable in terms of natural hierarchy
principles.

I don't follow the argument completely: the larger social system would
then be subsumed under the individual system (because of its larger size
and speed), but it is a social construction on top of the individuals,
isn't it? Is there room for a local inversion of the hierarchy (and thus of
the second law?) such as the generation of redundancy?

Best,

Loet

·Inga Ivanova and Loet Leydesdorff, Redundancy Generation in
University-Industry-Government Relations: The Triple Helix Modeled,
Measured, and Simulated. http://arxiv.org/abs/1308.3836

·Loet Leydesdorff and Inga Ivanova, Mutual ```

### Re: [Fis] reply to Loet

```Loet -- You wrote:

This is the case for natural systems and engineered systems (Herbert
Simon). However, above the individual the hierarchy is inverted because
collectively the communication is faster than the individual can
reflexively follow.

S: In general, while smaller scale systems can accelerate more quickly than
large scale ones, large scale ones are capable of greater absolute rates of
speed. Now, I gather that you are here speaking of non-natural systems --
i.e., human mechanical arrangements and social constructions.  It is a
complex question, but I will venture the possibility that what is happening
here is NOT acceleration, but absolute speeds, which in larger scale
systems can be faster. As a possible example, consider a firearm. The
bullet seems to be of small scale, and this might match its initial
acceleration, but its continued speed would be the speed of the large scale
social system that constructed it.

The complexity and speed of communication can be enhanced by codification.
The cultural system operates in terms of expectations (from the perspective
of hindsight) and therefore against the entropy law.

S: (Nothing can go against the 'entropy law'.)  A nice example for you
might be communication over distances by flashing lights using the Morse
code.  The actual local operations here may not be the best framework to
view this (including in thermodynamic terms). Again, I could subsume this
example into my above argument -- that is, it is the social system that is
communicating, not individual persons.  It takes two positions for this
communication to occur, and this makes the system a large scale one, and so
its speed of communication is understandable in terms of natural hierarchy
principles.

Then... Krassimir wrote:

The concept “window” not exactly correspond to reality.
Building the “hierarchy”, the Nature uses “structuring” of low levels to
build upper ones.

S: This building from 'bottom-up' is only part of the system. Everything
exists somewhere, and so, your bottom was somewhere too before it started
building upwards. This somewhere was its physical context, which will have
imposed various boundary and initial conditions upon the building process.
This is sometimes called 'downward causation'. So the new level built
would be a level in between the original upper (constraining) and lower
(building) levels.

What we call “window” is the set of elements which are “used” to create the
new level entities with “emergent” features.

S: And what that window 'saw' was the various initial and boundary
conditions that would be imposed upon the building.

STAN

In other words, “channels” do not exist but chains of “structuring” and
“restructuring” processes.

On Fri, Nov 1, 2013 at 8:20 AM, Loet Leydesdorff l...@leydesdorff.netwrote:

S: Yes. These 'windows' are the channels for constraint imposition from
level to level -- transactions, not direct interactions -- between them.
The lower, faster acting, level provides 'data' constructed as ensemble
data by the higher level, while the higher level imposes relatively
continuous constraints upon the lower level.

In short, there IS need for hierarchy, properly understood.

** **

Dear Stan,

** **

This is the case for natural systems and engineered systems (Herbert
Simon). However, above the individual the hierarchy is inverted because
collectively the communication is faster than the individual can
reflexively follow. The complexity and speed of communication can be
enhanced by codification. The cultural system operates in terms of
expectations (from the perspective of hindsight) and therefore against the
entropy law.

** **

Thanks otherwise!

** **

Best,

Loet

** **

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### Re: [Fis] Praxotype

```Kark, all -- I have question about this numbers -- words concept.  For
users of a given language much an be communicated by connotation as well as
denotation.  It seems to me that the matching of numbers to words would not
encompass this -- would it?  As well, what about synonyms with slightly
diifferent meanings?

STAN

On Tue, Oct 15, 2013 at 8:32 AM, Karl Javorszky karl.javors...@gmail.comwrote:

Cointinuing Bob's discourse on language and words, the next step was done
by Wittgenstein, who said that as tokens, words can be represented by
numbers. This is a resurrecting of Pythagoras' statement, that Nature is
representable by natural numbers and their harmonies.
It is important to keep in mind that numbers have as many
interrelationships among each other as words - if not more. And, by the use
of computers, we can make their harmonies among each other visible to the
human. The inner poetry of words that is behind the words themselves, can
be found in the relations among the natural numbers.
Karl

2013/10/15 Bob Logan lo...@physics.utoronto.ca

Thanks John for alerting us to the terms praxotype and cognotyppe. I have
a simpler formula which I made use of in my book the Extended Mind: The
Emergence of Language, the Human Mind and Culture. Words are simply
concepts and hence thinking tools. Before verbal language hominids
communicated by mimesis, i.e. hand signals, facial gestures, body language
and prosody (non-verbal vocalization) like grunts. As the complexity of
hominid existence increased mimesis did not have the requisite variety for
everyday life. Conceptualization was needed. Verbal language emerged in
which our words were our first concepts. The word water, for example, was a
concept that united all our percepts of the water we drank, washed with,
cooked with, fell as rain, or was found in rivers, lakes or the sea. With
language the brain which before was a percept engine bifurcated into the
human mind capable of conceptualization and hence planning and large scale
coordination. Verbal language allowed us to deal with matters not
immediately available in space and time. I claim that the emergence of
verbal language represented three simultaneous bifurcations: from mimetic
communication to verbal langauge; from the brain as a percept engine to the
mind capable of conceptualization and from hominids to fully human Homo
Sapiens.

for more details visit

or

cheers - Bob Logan

On 2013-10-15, at 2:54 AM, John Collier wrote:

This term might be useful in the context of the present discussion,
especially in the contest of coordinated practice(s). Cognotype might also
be useful. I think these might lead to a more fine-grained analysis of the
more integrative sociotype.
** **

http://blogs.scientificamerican.com/guest-blog/2013/09/27/words-are-thinking-tools-praxotype/

** **
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Robert K. Logan
Chief Scientist - sLab at OCAD
Prof. Emeritus - Physics - U. of Toronto
www.physics.utoronto.ca/Members/logan

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### Re: [Fis] THE SOCIOTYPE: SOCIAL RELATIONSHIPS AND BEYOND

```Krassimir -- you said:

Social organization is a separate level of living matter hierarchy with
specific “emerged” [Ashby] features.

There is no direct “smooth” transition from one level of living matter to
another.

What is common for all levels of living matter organization are the
“information phenomena and processes” which (of course!) are specific for
different levels.

I understand your  hierarchy to be a subsumptive one -- thus:

{physical realm {material realm {biological realm {socioeconomic realm.
Your statements are correct in this context.

STAN

On Tue, Oct 8, 2013 at 1:21 PM, Krassimir Markov mar...@foibg.com wrote:

Dear Raquel, Loet and FIS Colleagues,

Yes, “global brain” is mystification.

One may find similarity between organization of society and human brain.

But this is the same kind of similarity as to mechanism, computer, clock,
etc. .

Such similarities may be used to generate some new ideas or to break down

Social organization is a separate level of living matter hierarchy with
specific “emerged” [Ashby] features.

There is no direct “smooth” transition from one level of living matter to
another.

What is common for all levels of living matter organization are the
“information phenomena and processes” which (of course!) are specific for
different levels.

Because the information is a kind of reflection and the reflection is
attribute of the matter.

If one ask me what is the “emerged” feature of human society, my answer
will be “the natural languages” and information interaction based on
linguistic constructions.

Friendly regards
Krassimir

*From:* Loet Leydesdorff l...@leydesdorff.net
*Sent:* Tuesday, October 08, 2013 5:11 PM
*To:* 'Raquel del Moral' rdelmoral.i...@aragon.es ; fis@listas.unizar.es
*Subject:* Re: [Fis] THE SOCIOTYPE: SOCIAL RELATIONSHIPS AND BEYOND

Loet, your criticism is very accurate, thanks. But I really think, as said
Jorge, that our sociality has to have a fairly stable structure, that is
to say, lower and upper limits that feed our mental wellbeing. It's not
fixed,
of course, but individuals become integral embodiments of emotions, and
most of the active components of these emotions reside in our social
environment. Evolutionarily we have developed this social dependence, and
therefore the absence of such bonds, or the feeling of not having them, is
devastating to our health --both physical and mental, as emphasized by
numerous
studies.

Dear Raquel:

Expectations of social structure are extremely stable without
materialization. For example, the expectation of the rule of law. These are
anchored/reflected in codes of communications. One does not have to appeal
to a “global brain”. It seems a mystification to me.

Of course, the social expectations when codified leave footprints behind
in the form of institutions. For example, courts and parliaments as places
where one enacts the rule of law.

Best,

Loet

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### Re: [Fis] [Fwd: SV: Science, Philosophy and Information. An Alternative Relation] S.Brier

```Søren -- Your science without philosophy is what we have mostly been
having since the industrial revolution.  In this period sciences has mostly
been the handmaid of engineering and technology, following Francis Bacon's
recommendation.  Now that our culture has captured and partly destroyed
much of the world, it is time to regain a philosophical grip on the
'sorcerer's apprentice'! One tool for this is to reinstate final cause and
Aristotle's four causes analysis.

STAN

On Mon, Feb 11, 2013 at 10:28 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Original Message
Subject:SV: [Fis] Science, Philosophy and Information. An
Alternative
Relation
Date:   Thu, 07 Feb 2013 20:32:04 +0100
From:   Søren Brier sb@cbs.dk
To: joe.bren...@bluewin.ch joe.bren...@bluewin.ch, Pedro Clemente
Marijuan Fernandez pcmarijuan.i...@aragon.es, fis@listas.unizar.es
fis@listas.unizar.es, John Collier colli...@ukzn.ac.za
References: 6043399.89641360255002322.javamail.webm...@bluewin.ch

Dear Joseph

I go for each of the three nominally independent disciplines are not
independent, but that each provides a dynamic ontological and
epistemological link to the other two, more or less strong or actual
depending on the extent to which one wishes to emphasize certain aspects
of knowledge. Science without philosophy is stupid but philosophy
without science is blind. I am for a synergetic interaction.

Best wishes

Søren Brier

Professor in the semiotics of information, cognition and commmunication
science,

School,

Dalgas Have 15, 2000 Frederiksberg, Denmark,

*Fra:* fis-boun...@listas.unizar.es
[mailto:fis-boun...@listas.unizar.es] *På vegne af *joe.bren...@bluewin.ch
*Sendt:* 7. februar 2013 17:37
*Til:* Pedro Clemente Marijuan Fernandez; fis@listas.unizar.es; John
Collier
*Emne:* [Fis] Science, Philosophy and Information. An Alternative Relation

Dear FIS Colleagues,

The formation of the the Society for the Philosophy of Information at
the University of Hertfordshire is announced in the link in John's note.
It includes the announcement and Call for Papers of the International
Conference on the Philosophy of Information to be held in Xi'An, China
in October, 2013, sponsored by both the above Society, led by Professor
Luciano Floridi and the Institute for the Philosophy of Information in
Xi'An under the direction of Professor Wu Kun.

This increased activity in the area of the philosophy of information
(another major Workshop is planned this Spring) raises the issue of the
relation between the science and philosophy of information as well as of
the philosophy of science. I am aware of and agree with the position
expressed by Pedro that information science in the FIS framework should
emphasize scientific research in the sense of knowledge that is
quantifiable and/or provable. However, I do not believe that either he
or others of you intend to exclude rigorous qualitative knowledge,
especially as it concerns the dual nature of information.

The ubiquitous presence of information in all disciplines, as emphasized
by Wu, suggests an alternative relation linking philosophy, science and
information that is NOT one of simple hierarchical inclusion or
possession (of). One possibility is to say that it is information that
links philosophy and science, but this formulation perhaps fails to
recognize the general properties of the latter two.

Another possibility is to say that each of the three nominally
independent disciplines are not independent, but that each provides a
dynamic ontological and epistemological link to the other two, more or
less strong or actual depending on the extent to which one wishes to
emphasize certain aspects of knowledge.

I look forward to your comments regarding the pros and cons of such a
conception. Thank you.

Best wishes,

Joseph

Ursprüngliche Nachricht
Von: colli...@ukzn.ac.za mailto:colli...@ukzn.ac.za
Datum: 04.02.2013 18:57
An: fisfis@listas.unizar.es mailto:fis@listas.unizar.es
Betreff: [Fis] Society for the Philosophy of Information

http://www.socphilinfo.org/

--
Professor John Collier
colli...@ukzn.ac.za mailto:colli...@ukzn.ac.za
Philosophy and Ethics, University of KwaZulu-Natal, Durban 4041 South
Africa
T: +27 (31) 260 3248 / 260 2292   F: +27 (31) 260 3031
http://web.ncf.ca/collierhttp://web.ncfhttp://web.ncf.ca/collier
.ca/collier
http://web.ncf%3chttp:/web.ncf.ca/collier%3e.ca/collier

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Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la ```

### [Fis] Fwd: It's (Almost) Alive! Scientists Create a Near-Living Crystal | Wired Science | Wired.com

```-- Forwarded message --
From: Malcolm Dean malcolmd...@gmail.com
Date: Sun, Feb 3, 2013 at 11:14 PM
Subject: Fwd: It's (Almost) Alive! Scientists Create a Near-Living Crystal
| Wired Science | Wired.com
To: Stanley N. Salthe ssal...@binghamton.edu

-- Forwarded message --
From: Malcolm Dean malcolmd...@gmail.com
Date: Feb 3, 2013 2:25 PM
Subject: It's (Almost) Alive! Scientists Create a Near-Living Crystal |
Wired Science | Wired.com
To: Malcolm Dean malcolmd...@gmail.com
Cc:

http://www.wired.com/wiredscience/2013/01/living-crystal/
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### [Fis] dark matter

```Gordana has said:

Information and Energy/Matter

What can we hope for from studies of information related to energy/matter
(as it appears for us in space/time)? Information is a concept known for
its ambiguity in both common, everyday use and in its specific technical
applications throughout different fields of research and technology.
However, most people are unaware that matter/energy today is also a concept
surrounded by a disquieting uncertainty. What for Democritus were building
blocks of the whole universe appear today to constitute only 4% of its
observed content. (NASA 2012) [1] The rest is labeled “dark matter”
(conjectured to explain gravitational effects otherwise unaccounted for)
and “dark energy” (introduced to account for the expansion of the
universe). We do not know what “dark matter” and “dark energy” actually
are. This indicates that our present understanding of the structure of the
physical world needs re-examination. [...]

Information and Energy/Matter
Gordana Dodig Crnkovic

Information 2012, 3(4), 751-755;
http://unam.us4.list-manage2.com/track/click?u=0eb0ac9b4e8565f2967a8304bid=ae24f18d1ee=d38efa683e

Special Issue Information and Energy/Matter

http://unam.us4.list-manage.com/track/click?u=0eb0ac9b4e8565f2967a8304bid=ea193b9747e=d38efa683e

See it on Scoop.it (
http://unam.us4.list-manage.com/track/click?u=0eb0ac9b4e8565f2967a8304bid=cdfa764e97e=d38efa683e)
, via Papers (
http://unam.us4.list-manage.com/track/click?u=0eb0ac9b4e8565f2967a8304bid=e23b9e2cd9e=d38efa683e
)

I would like to inquire whether any fis'rs might react to the following
notion:

Dark matter is postulated because the amount of matter detectable in
galaxies would be insufficient alone to explain how they hold together
given the value of the gravitational constant.

However, the information we glean from galaxies represents their condition
as it was a very long time ago, in an earlier universe.

Is it not possible to resolve this puzzle less radically than by inventing
dark matter by supposing that the gravitational constant has not been
constant but has instead been changing, and was much stronger in the past,
which is when we detect these distant clusters of matter?  Perhaps G as
been scaled to the rate of expansion of space?  Perhaps the rate of
expansion was greater then than now, even with current acceleration?

STAN
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### Re: [Fis] The Information Flow

```Bruno said --
but this does not mean that Mechanism is
a good *explanation* of anything. On the contrary, I prefer to look at
it as a tool, perhaps a simplifying tool, to *formulate* the problems
(notably the mind-body problem), to explain it is not yet solved, even
in that simplifying frame, etc.

Quite right.  Logic is a linguistic mechanism, and a ll of our
philosophical and scientific efforts are mediated by it.  We (except poets)
are all mechanists!

STAN

On Tue, Nov 13, 2012 at 8:50 AM, Bruno Marchal marc...@ulb.ac.be wrote:

Dear Robert and FIS colleagues,

On 12 Nov 2012, at 16:35, Robert Ulanowicz wrote:

Dear Pedro,

Roman  Littlefield is coming out with a volume along those lines
entitled Beyond Mechanism

As for our Chinese colleagues, I find them more open to non-mechanical
scenarios than are anglophones.

The problem is that few people defending mechanism are aware that
mechanism is incompatible with weak materialism (the primary existence
of a physical universe, that is more or less the current dogma/
paradigm). Most proponents of Mechanism have still the 19th century
conception of Mechanism, which is refuted by theoretical computer
science/mathematical logic.

Mechanical entities are intrinsically related to non mechanical
scenario. You cannot genuinely be open to mechanism without being open
to the non-mechanical. Most predicate applying to machine are
undecidable, non mechanical, etc. Machines, notably when they are self-
observing, are confronted to the non mechanical, and *can* overcome it
by relying on non mechanically generable informations.

I am not defending Mechanism, but as a logician I do invalidate
widespread misconception on machines, and notably I try to explain
that Digital Mechanism (computationalism) is quite the opposite of
reductionism. I would even say that it might be used as a vaccine
against reductionism in the exact and human science.

Mechanism, in the weak sense I am using, is quite plausible, as there
are no evidences against it, but this does not mean that Mechanism is
a good *explanation* of anything. On the contrary, I prefer to look at
it as a tool, perhaps a simplifying tool, to *formulate* the problems
(notably the mind-body problem), to explain it is not yet solved, even
in that simplifying frame, etc. We are very ignorant of what are
machines, and probably so, in case we assume we are ourself Turing
emulable (with or without oracles).

All three of my books are being
translated into Chinese. The first one, Growth and Development:
Ecosystems Phenomenology has already been published.

Congratulation !

Best,

Bruno

Quoting PEDRO CLEMENTE MARIJUAN FERNANDEZ pcmarijuan.i...@aragon.es:

Dear colleagues,

Yes, the foundations are trembling... as usual during quite long a
time. Maybe too many aspects have to be put into line in order to
have new, more consistent foundations for human knowledge. Until now
the different crisis of Mechanics, the dominant scientific culture,
have been solved at the small price of leaving conceptual
inconsistencies until the rug of brand new fields or subdisciplines
while at the same time fictive claims of unity of sceince,
reductionism, etc. were upheld. Good for mechanics, as probably
there were few competing options around --if any. Bad for the whole
human knowledge, as multidisciplinary schizophrenia has been
assumed as the natural state of mental health.

My opinion is that information science should carefully examine the
problematic claims at the core of mechanical ways of explanation, as
some (many?) of them refer to the information stuff: unlimited
communication (even between physical elements), arbitrary partitions
and boundary conditions, ideal status of the acting laws of nature,
ominiscient observer, idealized nature of human knowledge  (no
neurodynamics of knowledge), disciplinary hierarchies versus
heterarchical interrelationships, logical versus social construction
and knowledge recombination, idealized social information, etc.etc.
Probably I have misconceived and wrongly expressed some of those
problems, but in any case it is unfortunate that there is a dense
feedback among them and a strong entrenchment with many others, so

The big problem some of us see, and I tried to argument about that
in the last Beijing FIS meeting, is that without an entrance of some
partial aspect in the professional science system, none of the
those challenges has the slightest possibility of being developed in
the amateur mode/marginal science our studies are caught into.
Therefore a common challenge for FIS, the new ISIS society, ITHEA,
Symmetrion, INBIOSA, etc. is to take some piece or problem, with
practical implications, and enter it into the institutional ```

### Re: [Fis] The Information Flow

```Pedro -- The Aristotelian causal categories are conceptual tools, providing
language for distinguishing aspects of a scene.  Without them we are liable
to miss certain aspects of nature. For example, Francis Bacon eliminated
final cause from science discourse, explicitly stating that finality can
only apply to human needs. This eliminated much in nature -- in fact those
aspects not useful for the construction of machines.  Note that
experimental science -- most of physics -- embodies formal and final causes
in the construction of an experimental setup, eliminating these categories
from the observation of what happens when an observed system is stimulated
by an efficient cause (to be noted only afterward in 'materials and
methods').  Thus, formal and final causes tend to become invisible.  This
is valid in physics, or any experimental science which seeks to discover
the possibilities of observed systems, and not to explain actual phenomena
(which are mostly influenced by historically determined nonholonomic
constraints and context (formal causes).

The fact that 'what, how and where' may be transported along one route in a
natural system cannot eliminate them as conceptual tools.

STAN

On Fri, Oct 26, 2012 at 4:32 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ
pcmarijuan.i...@aragon.es wrote:

Dear FISers,

Is it interesting the discussion on wether those informational entities
contain realizations of the Aristotelian scheme of causality or not?

The cell, in my view, conspicuously fails --it would be too artifactual an
scheme. Some parts of the sensory paths of advanced nervous systems seem to
separate some of those causes --but only in a few parts or patches of the
concerned pathway. For instance, in visual processing the what and the
how/where seem to be travelling together undifferentiated along the optic
nerve and are separated --more or less-- after the visual superior
colliculus in the midbrain before discharging onto the visual cortex. The
really big flow of spikes arriving each instant (many millions every few
milisec) are mixed and correlated with themselves and with other top-down
and bottom-up preexisting flows in multiple neural mappings... and further,
when those flows mix with the association areas under the influence of
languaje, then, and only then, all those logic and conceptual
categorizations of human thought are enacted in the ephemeral synaptic
networks.

I am optimistic that  a new Heraclitean way of thinking boils down in
network science, neuroinformatics, systems biology, bioinformation etc.
Neither the Parmenidean eliminative fixism of classical reductionists,
nor the Aristotelian organicism of systemicists. Say that this is a
caricature. However you cannot bathe twice in the same river not just
because we all are caught into the universal physical flow of photons and
forces, but for the Heraclitean flux of our own neurons and brains, for
the inner torrents of the aggregated information flows. The same for
whatever cells, societies, etc. and their physical structures for info
transportation.

Either we produce an interesting new vision of the world, finally making
sense of those perennial metaphors among the different (informational)
realms, or information science will continue to be that small portion of
incoherent patches more or less close to information theory or to
revolution and information society and tons of ad hoc literature, the
educated thought of our contemporary society continues to be deeply
mechanistic!

Why?

best wishes

---Pedro

-snip-

I think it of some interest that I have
previously ( 2006  On
Aristotle’s conception of causality.
General Systems Bulletin 35:
11.) proposed that the Aristotelian 'formal
cause' determines both
'what happens' and 'how it happens', and that
the combination of
this with material cause ('what it happens
to') delivers 'where' it
happens.

(For completeness sake I add that efficient
cause determines only
'when it happens', while final cause points
to 'why it happens'.  It
would be quite exciting to find that these
informations were also
carried on separate tracts.)

It would be exciting, as that would seem to refute the
Aristotelean idea
of the four causes as four aspects of all causation. However an
information channel can carry some part of the information from
its
source, which would be a sort of filter or abstraction of the
source.
So, for example, a channel might be sensitive only to the how,
but not
the what, and vice versa. A channel is fundamentally a mapping
of
classes from a source to a sink that through instances that
retain the
mapping (see Barwsie and Seligman, Information Flow: The Logic
of
Distributed Systems). So in this case, a channel sensitive to,
say,
what, would retain the what ```

### Re: [Fis] The Information Flow

```Pedro -- it is of interest to me that

On Sun, Oct 21, 2012 at 3:38 PM, PEDRO CLEMENTE MARIJUAN FERNANDEZ
pcmarijuan.i...@aragon.es wrote:

Dear FISers,

Continuing with the comments on the how versus the what, it is an
important topic in mammalian (vertebrate) nervous systems. They are
subtended by mostly separate neural tracts (though partially
interconnected), it is the dorsal stream, specialized in the how  where,
and the ventral stream stream about the what.

-snip-

I think it of some interest that I have previously ( 2006  On Aristotle’s
conception of causality.  General Systems Bulletin 35: 11.) proposed that
the Aristotelian 'formal cause' determines both 'what happens' and 'how it
happens', and that the combination of this with material cause ('what it
happens to') delivers 'where' it happens.

(For completeness sake I add that efficient cause determines only 'when it
happens', while final cause points to 'why it happens'.  It would be quite
exciting to find that these informations were also carried on separate
tracts.)

STAN

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### Re: [Fis] FW: [Fwd: Re: Physics of computing]--Plamen S.

```Concerning the meaning (or effect) of information (or constraint) in
general, I have proposed that context is crucial in modulating the effect
-- in all cases.  Thus: it would be like the logical example:

Effect = context a   x   Constraint ^context b

STAN

On Fri, Mar 16, 2012 at 2:18 PM, Christophe Menant
christophe.men...@hotmail.fr wrote:

*Dear FISers,
Indeed information can be considered downwards (physical  meaningless)
and upwards (biological  meaningful). The difference being about
interpretation or not.
It also introduces an evolutionary approach to information processing and
meaning generation.
There is a chapter on that subject in a recent book (
http://www.amazon.co.uk/Information-Computation-Philosophical-Understanding-Foundations/dp/toc/9814295477
).
“Computation on Information, Meaning and Representations.An Evolutionary
Approach”
Content of the chapter:
1. Information and Meaning. Meaning Generation
1.1. Information.Meaning of information and quantity of information
1.2. Meaningful information and constraint satisfaction. A systemic
approach
2. Information, Meaning and Representations. An Evolutionary Approach
2.1. Stay alive constraint and meaning generation for organisms
2.2. The Meaning Generator System (MGS). A systemic and evolutionary
approach
2.3. Meaning transmission
2.4. Individual and species constraints. Group life constraints. Networks
of meanings
2.5. From meaningful information to meaningful representations
3. Meaningful Information and Representations in Humans
4. Meaningful Information and Representations in Artificial Systems
4.1. Meaningful information and representations from traditional AI to
Nouvelle AI. Embodied-situated AI
4.2. Meaningful representations versus the guidance theory of
representation
4.3. Meaningful information and representations versus the enactive
approach
5. Conclusion and Continuation
5.1. Conclusion
5.2. Continuation
A version close to the final text can be reached at
http://crmenant.free.fr/2009BookChapter/C.Menant.211009.pdf

As Plamen says, we may be at the beginning of a new scientific revolution.
But I’m afraid that an understanding of the meaning of information needs
clear enough an understanding of the constraint at the source of the
meaning generation process. And even for basic organic meanings coming from
a “stay alive” constraint, we have to face the still mysterious nature of
life. And for human meanings, the even more mysterious nature of human mind.
This is not to discourage our efforts in investigating these questions.
Just to put a stick in the ground showing where we stand.
Best,
Christophe
*
--
Date: Fri, 16 Mar 2012 13:47:28 +0100
From: pcmarijuan.i...@aragon.es
To: fis@listas.unizar.es
Subject: [Fis] [Fwd: Re: Physics of computing]--Plamen S.

Mensaje original   Asunto: Re: [Fis] Physics of computing
Fecha:
Fri, 16 Mar 2012 13:24:38 +0100  De: Dr. Plamen L. Simeonov
plamen.l.simeo...@gmail.com plamen.l.simeo...@gmail.com  Para: Pedro
C. Marijuan pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es
Referencias:
20120316041607.66ffc68000...@1w8.tpn.terra.com20120316041607.66ffc68000...@1w8.tpn.terra.com
4f6321c3.5000...@aragon.es 4f6321c3.5000...@aragon.es

+++

Dear All,

I could not agree more with Pedro's opinion. The referred article is
interesting indeed. but, information is only physical in the narrow sense
taken by conventional physicalistic-mechanistic-computational approaches.
Such a statement defends the reductionist view at nature: sorry. But
information is more than bits and Shanno's law and biology has far more to
offer. I think we are at the beginning of a new scientific revolution. So,
we may need to take our (Maxwell) daemons and (Turing) oracles closer
under the lens. In fact, David Ball, the author of the Nature paper
approached me after my talk in Brussels in 2010 on the Integral Biomathics
approach and told me he thinks it were a step in the right direction:
biology driven mathematics and computation.

By the way, our book of ideas on IB will be released next month by
Springer:
http://www.springer.com/engineering/computational+intelligence+and+complexity/book/978-3-642-28110-5
If you wish to obtain it at a lower price (65 EUR incl. worldwide
via email to: pla...@simeio.org. There must be at least 9 orders to keep
that discount price..

Best,

Plamen

On Fri, Mar 16, 2012 at 12:19 PM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Dear discussants,

I tend to disagree with the motto information is physical if taken too
strictly. Obviously if we look downwards it is OK, but in the upward
direction it is different. Info is not only physical then, and the
dimension of self-construction along the realization of life cycle has to
be entered. Then the signal, the info, has content ```

### Re: [Fis] THEORY AND SCIENCE From QTQ

```Bob -- Agreed. The way I see it is that there are two orientations in
science, and these depend upon personality.  One is the strategy of
confirmation (of a favored theory), the other is the strategy of testing
(of other's theories).  The gist of confirmation is to conjure, and then
firm up, a concept with increasing examples (this fits my own, basically
artistic, temperament).  The gist of testing, as Popper persuaded us, is to
try to destroy any theory, with the notion that all of them would
eventually get overturned. This fits with pessimistic personalities. This
view seems inconsistent with the now-getting-popular idea from C.S. Peirce,
that we will discover 'truth' in the long run.  Of course, from semiotics
we also have the view (originally from von Uexküll) that each species is
locked into its own sensorium (and so each culture into its own linguistic
and conceptual biases as well), meaning that this truth could only be one
possible version of the world.  (Note that technological effectiveness
cannot suggest that a theory is 'true', even though many scientists believe
this.)

STAN

On Wed, Jan 11, 2012 at 9:49 AM, Bob Logan lo...@physics.utoronto.cawrote:

Caro Colleagues - Etymology is always a useful exercise - theory and
theatre come from the same root 'to see' and science from the root 'to
know'. The word *theoria* θεωρία, meant 'a looking at, viewing,
beholding', and referring to contemplation or speculation (wikipedia
article on theory). Now most often we say to see is to believe or know.
This translate into the idea that  theory helps us to believe or to know or
to do science. But Marshall McLuhan said I did not see it until I believed
it. In other words to believe or know is a necessary condition to be able
to see which translates into the idea that we need science to make a
theory. Science is a way of organizing theories and theories are a way of
organizing science. The relation of science and theory is a chicken and egg
problem. It is a question of emergence. The relation of science and theory
is one of non-linear dynamics. One needs science to make a theory and a
theory or theories to make science. As is the case with emergent phenomena
one cannot predict what theories will emerge from science or what science
will emerge from theories. This is my theory of science and my science of
theories.

I hope you enjoyed my playful take on the relation of science and theory
which I offer as a serious resolution to the challenges raised in this
thread. I also hope you will comment.

with kind regards - Bob Logan

On 2012-01-11, at 2:42 AM, Krassimir Markov wrote:

Dear QTQ and FIS Colleagues,

I am afraid we had not define the terms ‘theory” and “science” but start
discussion.
Let firstly clear what they means and after that to make conclusions.

It is clear the theories are part of the science but the science is
something more.

In our area - the Information Science is quite more than any theory for
information.

Of course,  “What is information?” is the basic question, but after it
follow the questions “How it is used by live organisms?” and “Why it is
needed for social structures?”, “Why one and the same reflection is
information for one but not for another subject?” and “Can the information
be totally destroyed or not, i.e. is the information depended with physical
(material) world or not?”, etc.

---

I have more than 35 year experience in editing and publishing scientific
collections and journals.
My personal position is: “The Variety and Independence cause Development!”

Every journal has its own politic and there is no sense to discus its
rules.
My personal position is presented in the name of my firs Int. Journal:
“Information Theories and Applications”.
Yes – Theories.

Some scientists prefer to be protected from “spam” papers by the
reviewers, but this has simple decision – “Do not read papers at all !”

The science needs new ideas.
Sometimes the proper way is not in the fat books but in the thin papers.
We have long history of development but are we sure that all in it
(especially for information) is absolutely correct ant may be accepted
without doubt?

---

Happy New 2012 Year!
Friendly regards

Krassimir

*From:* Pedro C. Marijuan pcmarijuan.i...@aragon.es
*Sent:* Tuesday, January 10, 2012 5:48 PM
*To:* fis@listas.unizar.es
*Subject:* [Fis] [Fwd: THEORY AND SCIENCE] From QTQ

Mensaje original   Asunto: THEORY AND SCIENCE Fecha: Tue,
10 Jan 2012 10:49:58 +0800 De: whhbs...@sina.com Responder a:
whhbs...@sina.com Para: Pedro C. Marijuan
mailto:pcmarijuan.i...@aragon.espcmarijuan.i...@aragon.es,
mjs mailto:m...@aiu.ac.jp m...@aiu.ac.jp, Joseph Brenner
mailto:joe.bren...@bluewin.ch joe.bren...@bluewin.ch, fislist
mailto:fis@listas.unizar.es fis@listas.unizar.es

Dear Pedro, Dear Marcin, Dear Joseph, Dear FIS Colleagues,
Theory is important and necessary, but theory ```

### Re: [Fis] Discussion of Information Science Education

```And it could feature in 'Science for Non-Majors' courses as well.

STAN

On Mon, Dec 5, 2011 at 12:44 PM, Guy A Hoelzer hoel...@unr.edu wrote:

Hi All,

I agree with those who are suggesting that Information Science makes sense
as a widely useful way to think about different scientific disciplines
even if we don't have a strong consensus on how to define 'information'.
I think there is enough coherence among views of 'information' to underpin
the unity and universality of the approach.  Perhaps Information Science
is less a discipline of its own and more of a common approach to
understanding that can be applied across disciplines.  While I can imagine
good courses focusing on Information Science, it might be most productive
to include a common framework for information-based models/viewpoints
across the curriculum.

Guy Hoelzer

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### Re: [Fis] Discussion of Information Science Education

```Regarding:

Information Science is a perfect tool for integration of curriculum,
especially in the context of Liberal Arts education. Which other concept,
if not information, can be applied in all possible contexts of education?

I would point out that there have been two previous disciplines that have
attempted this reasonable goal -- systems science and semiotics.  Neither
one ever became a major program except in one or two universities where
major players worked.  Our culture rewards specializations much more than
general applications.

STAN

On Sat, Dec 3, 2011 at 7:23 AM, m...@aiu.ac.jp wrote:

Dear Colleagues:
discussions without conclusive answers. For instance: What is
information? However, the lack of consensus regarding central
concept is not an obstacle in the development of Information
Science. There is no commonly accepted answer to the question
What is life? But, this does not threaten the identity of
Biology.

Information Science has not yet achieved a status of a
commonly recognized discipline. It is frequently confused with
Computer Science, because of the term Informatics which in
Europe denotes what in the US is called Computing, or with
Library
Science and sometimes even with Philosophy of Information,
as visible from the Handbook on the Philosophy of Information
http://www.illc.uva.nl/HPI/ where philosophy and science
interleave
on many levels.

Information Science will never receive recognition without an
organized effort of research community to introduce its
philosophy,
goals, methods, and achievements to the general audience.

Books and articles popularizing the theme of information as
a subject of independent study do not have big enough
circulation to be sufficient in establishing an identity of
the discipline. The only effective way is to introduce
Information Science as a subject of education at the college
level for students who do not necessarily want to specialize
in this direction.

Certainly, introduction of a new subject to curriculum is not
easy, but it is possible. After all, Information Science is a
perfect tool for integration of curriculum, especially in the
context of Liberal Arts education. Which other concept, if not
information, can be applied in all possible contexts of
education?

Now, the question is whether we are ready to come out with a
syllabus for such a course acceptable for all of us, those who
are involved in the subject, and those who aren't, but
participate in the development of curricula. Can we overcome
differences between our views on the definition of
information, on the relationship of information understood in
a general way to its particular manifestations in other
disciplines?

Since the course (or courses) should present an identity of
the discipline of Information Science, it is very important
that we are convinced about the authentic existence of a large
enough common ground. Can we develop a map of this territory?
Can we pool resources to establish foundations for a standard,
Information Science curriculum?

Marcin and Gordana

Marcin J. Schroeder, Ph.D.
Professor and Dean of Academic Affairs
Akita International University
Akita, Japan
m...@aiu.ac.jp

Gordana Dodig Crnkovic,
Associate Professor
Head of the Computer Science and Networks Department
School of Innovation, Design and Engineering
Mälardalen University
Sweden
http://www.mrtc.mdh.se/~gdc/

Organizer of the Symposium on Natural/Unconventional
Computing,
the Turing Centenary  World Congress of AISB/IACAP

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### Re: [Fis] Category Theory and Information. Back to Basics

```Joseph --

On Fri, Oct 28, 2011 at 3:37 AM, Joseph Brenner joe.bren...@bluewin.chwrote:

**
Dear Stan,

usual logics and the actual, changing world but that it is fatal only in
*those
*logics. Logic in Reality reduces to standard logic for simple process
phenomena involving minimal interactive aspects - those which
science handles easily. But LIR  applies to more complex phenomena whose
evolution I would not consider outside science. Could we say that LIR is a
way of bringing change better within science?

encompasses change as it happens. It describes logical characteristics
of the evolution of processes in a multi-dimensional configuration space.
The elements of the logic are changing values of the actuality and
potentiality of the elements in interaction (e.g., system and environment).
The
disjunction thus becomes, itself, a process describable by LIR.

So, just to get a clearer statement -- we can have a differential equation
describing some kind of change. But here the constants are fixed, and so the
change is predetermined, and used to describe only average, standard or
characteristic changes.  So, you seem to be saying that in LIR format one
can describe changes where the constraints are not fixed.

If so, would the changes of the constants be in some way predetermined?  Or
could that be open as well?

I do not expect that people who wish to retain the characteristics of
standard category theory can accept the above any more than those who
require that logic refer only to propositions and their truth-values. I
have said that a conceptual mathematical theory applicable to my Logic in
Reality is both possible in principle and desirable. I only insist that none
such yet exists, since what does exist is eliminative with respect to the
interactive realities LIR attempts to discuss, among them information.

Does the above comment give some hint of what would be required, or
accomplished by this math?

STAN

Cheers,

Joseph

- Original Message -
*From:* Stanley N Salthe ssal...@binghamton.edu
*To:* joe.bren...@bluewin.ch ; fis@listas.unizar.es
*Sent:* Tuesday, October 18, 2011 11:16 PM
*Subject:* Re: [Fis] Category Theory and Information. Back to Basics

Joseph --
SS: Your objection seems to me to imply a fatal disjunction between our
usual logics -- the basis of science -- and the actual (changing) world.
For example, in biological ontogeny we begin at one scale, and GRADUALLy
assemble a larger scale.  During this transition the system is ambiguous as
to scale.  It is CHANGE which faults our thinking here, not the idea that a
developing embryo can be modeled as existing at more than one scale.  I
suppose you can then tell us that your system of logic (LIR) takes care of
this, by encompassing change as it happens.  Yes?

STAN

For complex process phenomena such as information, involving
complementarity, overlap or physical interactions between elements, these
doctrines fail. The mathematical conceptualization they provide does not
capture the non-Markovian aspects of the processes involved for which no
algorithm can be written. If any algebra is possible, it must be a
non-Boolean one, something like that used in quantum mechanics extended to
the macroscopic level.

I have proposed a new categorial ontology in which the key categorial
feature is NON-separability. This concept would seem to apply to some of the
approaches to information which have been proposed recently, e.g. those of
Deacon and Ulanowicz. I would greatly welcome the opportunity to see if my
approach and its logic stand up to further scrutiny.

As Loet suggests, we must avoid confounding such a (more qualitative)
discourse with the standard one and translate meaningfully between them.
However this means, as a minimum, accepting the existence and validity of
both, as well as the possibility in principle of some areas of overlap,
without conflation.

Best,

Joseph

- Original Message -
*From:* Gavin Ritz
*To:* 'Joseph Brenner'
*Sent:* Tuesday, October 18, 2011 10:45 AM
*Subject:* RE: [Fis] Chemo-informatics as the source of morphogenesis -
bothpractical and logical.

Hi there Joseph

This takes us

back to the question of the primacy of quantitative over qualitative

properties, or, better, over qualitative + quantitative properties.

Is this not a good reason to use category theory and a Topos (part of an
object), does not the axiom of “limits” and the axiom of “exponentiation-
map objects” deal philosophically with “quantity and limit” and “quality and
variety” concepts respectively.

Is this not the goal of category theory to explain the concepts in a
conceptual mathematical way.

Regards

Gavin

This for

me is the real area for discussion, and points to the need for both lines

being```

### [Fis] Fwd: Chemical information: a field of fuzzy contours ?

```Michel -- Regarding:

Now, I ask you the following: please can you provide an extremely
simple example (the most simple you could imagine) of situation in
which you can say:  in this situation, information is ... .
Chemical information is welcome, but an example from physics would be
great, too. However, please, no biology example, that will be dicussed
at the occasion of a future session.

Would it not be the case that chemical information would relate to
catalysts?  That is, chemical scale configurations which have the property
of forming enabling constraints for some chemical bond alterations.  Then,
of course, at the physical level we have the fermion / boson transactions
that actually make up the basis of a chemical reaction.

STAN

On Fri, Sep 23, 2011 at 7:07 AM, Michel Petitjean
petitjean.chi...@gmail.com wrote:

Dear FISers,

Pedro raises several points.
Among them:

1. Chemoinformatics or Cheminformatics ?
Both terms are encountered. I would say that unless some authority
takes a decision, both terms will continue to be used.

2. Despite I gave an example of what could be cheminformation in a
concrete case, I did not tell what was exactly cheminformation in this
concrete case. I just asked the question of what it could be.
Now, I ask you the following: please can you provide an extremely
simple example (the most simple you could imagine) of situation in
which you can say:  in this situation, information is ... .
Chemical information is welcome, but an example from physics would be
great, too. However, please, no biology example, that will be dicussed
at the occasion of a future session.
These examples are expected to help us to define information in more
general situations.

3. The comparison Pedro did with symmetry is of interest: can anyone
define symmetry ?
During a long time, symmetry had in common with information that many
people attempted to define it in its own field, giving raise to many
particular definitions, but not to a common and widely accepted one.
Some years ago, although I needed to mention a definition of symmetry
in one of my papers, I was surprised that I could not find an unifying
one (symmetry is known since millenaries!!). Even in the book of Weyl
I did not find the expected one.
So, I decided to build my own one (Symmetry: Culture and Science,
2007, 18[2-3], 99-119; free reprint at
http://petitjeanmichel.free.fr/itoweb.petitjean.html
In fact, the group structure which is generally a priori imposed, is a
consequence of several properties that the definition should satisfy
to be in agreement with some obvious intuitive requirements (and so,
five different groups appear naturally, none of them being imposed a
priori). Of course, the proposed unifying definition applies to a
broad spectrum of situations, not only the geometric one: matrices,
functions, distributions, graphs, etc.
But that was possible because I already had knowledge of the many
definitions in particular domains or situations.

Thus I expect that that you will post several examples of information
in very simples cases.
From the analysis of these situations we should move forward.

E.g., for symmetry, one of the simple examples I gave was the set of
three points of the real line: if one point is the mid of the two
other, there is symmetry (in fact, it is a case of achirality, i.e.
indirect symmetry, because here we deal with reflections rather than
with rotations).
It would be great to have so simple situations for information in
chemistry or physics.

ll my best,

Michel.

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### Re: [Fis] Chemical information: a field of fuzzy contours ?

```Michel -- Organic chemistry was known to be the most difficult course in
Columbia University.  But I got interested in it, worked very hard
constantly, and I achieved an  'A'.  But what you say here indicates several
orders of magnitude more difficulty than what I played with in university.
For me this raises a question about the 'realms of nature', as in the
subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
Do you think one should place an 'organic realm' between chemical and
biological?  Or, otherwise, do you think it possible that there might be
organic realms out in the universe not entrained into biology?

STAN

On Sat, Sep 17, 2011 at 1:53 PM, Michel Petitjean
petitjean.chi...@gmail.com wrote:

Dear Joe, dear FISErs,

An organic chemist is able to predict a number of properties from the
structural formula, including much about reactivity of the compound.
But as you know, doing that properly is extremely difficult in a
number of cases, because the rules governing reactivity are much more
complicated that the ones which are taught at Universities, and the
number of rules expands rapidly each year. In fact, an experienced
Organic Chemist has in his head a so extraordinary rich collection of
rules and a so enormous knowledge that even many chemists which are
not Organicians cannot imagine the extent of this knowledge.
It is clear that the doing chemistry process derives from these
rules (these rules are chemical information), not only from the
formulas.
Since the 70's, some cheminformaticians tried to store that in
databases: reactions databases plus databases of reactivity rules for
computer sssisted synthesis or retrosynthesis, etc., then built
programmes intended to output proposals supposed to help the chemist.
As far as I know, the brain of the Organician is still by far much
more efficient than the best softwares which were produced.
So, I may tell that the information available in the brain of the
Organician is extremely difficult to store on computer, and it is even
very difficult to teach it, apart the very beginning.
There are examples other than reactivity. A huge of QSAR studies were
done in order to predict various physico-chemical properties of simple
chemical compounds, e.g., predicting from the structural formulas the
boiling temperatures of monofunctional compounds such as alcohols,
cetones, etc. at 20 C under 1 atm. But even in these apparently simple
cases, the chemical information we need to do that with an acceptable
accuracy is difficult to extract: the conclusions of such QSAR studies
cannot be applied to any alcohol or cetone (still assumed to be
monofunctional compounds), and it is even difficult to know the extent
of validity of the published empirical rules, concretely often
summarized by some regression coefficients.
The example of spectroscopic databases is also of interest. How
simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
compounds ? Starting from the structural formula, it is really hard to
simulate, e.g. a low resolution mass spectra. Most time, it was
attempted to extract rules from spectroscopic databases, then try to
predict the spectra of a compound absent from the database, or
conversely, retrieving the structural formula of a compound from its
spectra(s). Many such softwares were developped since the 70's (one of
the oldest ones is STIRS), but really the chemical information needed
to do that properly is very difficult to extract.
To conclude, I retain your example of crystallization: for sure when
we will able to retrieve from the structural formula H-O-H that water
under 1 atm should crystallize at 0 C, then for sure we will be ready
to predict more about crystallization of chemicals.

Best regards,

Michel.

2011/9/17 joe.bren...@bluewin.ch joe.bren...@bluewin.ch:
Dear Michel and FIS Colleagues,

This will be an interesting discussion, since the core nature and role of
information will be involved. Here is just one first point: to me, as a
chemist, chemical information is only secondarily an object capable of
being formalized, archived, etc. A formula has meaning for me in terms
of the potential reactions the molecule to which it refers can undergo,
what
it looked like when crystallized for the first time and so on.

Cheminformatics seems not to deal with such aspects of chemical
information
as part of a process of doing chemistry. Can this be captured by
another system?

Best wishes,

Joseph

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### [Fis] testing

```I am having problems communicating with lists, So I am trying to see if this
gets through.

STAN
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### Re: [Fis] ON INFORMATION THEORY--Mark Burgin

```Replying to Gavin -- I think you make the 'error of misplaced concreteness'.
Information theory -- and all theories and laws are modeling tools, not
actual phenomena.  So, it is also true that when an apple falls it is not
being pulled by gravitation.  Gravitation is our way of understanding the
falling.  We all know these things, so it seems to me that there is no need
to point this out.

STAN

On Sat, Apr 9, 2011 at 11:45 PM, Gavin Ritz garr...@xtra.co.nz wrote:

Ted

Thank you Mark. This promises to be interesting.

My view may best be introduced by stating that I believe we are in the
business of creating a new science that will depend on new abstractions.
These abstractions will extend from the notion of information as a first
class citizen, as opposed to our default, the particle. The latter has
qualities that can be measured and in fact the very idea of metrics is
bound
to this notion of thingness.

GR: I just can't see the evidence that information has anything to do with
living organisms.

Much of the dialog here works with the problem of naming what that it is.

GR: They look more like logical operators, such as Imperative logic,
declarative logic and interrogative logic.

Having said that...

1.Is it necessary/useful/reasonable to make a strict
distinction between information as a phenomenon and information measures as
quantitative or qualitative characteristics of information?

I am rather certain that there is a very real distinction, because of how
we
define the problem. After all, we are not asking how do information and
information metrics fit within the confines of rather limited abstractions.
At least I am not. But the distinction does not allow for full
orthogonality
from set theory (the formalism of things), because we want to be able to
model and engineer observable phenomenon in a cleaner way. This should be
the test of any serious proposal, in my view.

This requirement is why discussion on these matters often moves into
category theory,

GR: It moves into Category theory and Topos my guess is because it's the
very basic framework of logic.

2.Are there types or kinds of information that are not
encompassed by the general theory of information (GTI)?

GR: for one no living organism uses Information theory constructs to
communicate with each other. ie direct languaging.

GR: Information theory is a construct used by our society to control
machines.

3.Is it necessary/useful/reasonable to make a distinction
between information and an information carrier?

GR: Only if we can find direct scientific evidence that organisms use
information theory constructs to communicate directly. So far none has been
found.

Clearly there is a system-level conveyance of information

GR: It's not so clear. If I can be pointed to one experiment that proves
there is such a thing as information theory constructs within living
organism I will be very excited.

that carries an organizational imperative.

GR: More like DNA is an Imperative logical operator.

I am intrigued by the notion introduced here recently that suggests
intelligence as inhabiting this new, non-parametrizable space.

GR: oops.

Regards
Gavin

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### [Fis] exchanges with Gordana

```On Fri, Apr 1, 2011 at 4:12 PM, Gordana Dodig-Crnkovic
gordana.dodig-crnko...@mdh.se wrote:

Dear Stan,

Ø  The key is whether the trait involved can be modeled; on these grounds it
has not yet been shown that 'qualia' can be generalized beyond the human
experience, yet even  a child can see, for example, that a mother hen is
very unhappy when her chicks are threatened.

Being a computer scientist I don’t really know enough about qualia, so I

“Examples of qualia are the pain of a headache, the taste of wine, the
experience of taking a recreational drug, or the redness of an evening sky.”

I believe that hen and other animals have some sort of qualia, of course not
human qualia, but their own, animal qualia.

Am I wrong in my believe that animals can feel pain, have headache, feel
taste of drink and food, can see colors and can even get drunk (Animals Are
Beautiful People,

that they experience represent their qualia?

With best regards,

Gordana

Gordana -- Of course, you are right.  My point is only that, while we can
intuit that other animals have feelings insofar as they have nerves, my
position, using Peirce's idea of Firstness, is that it is the simplest
hypothesis to suppose that all dissipative structures (storms, etc.,
including the living) have all that we have.  So a cyclone, a tree, must be
supposed to have at least what we would feel when, for example, we meditate
-- no thoughts, no special feelings, just beingness.  BUT, as we have no
model for this, so we are not entitled, as scientists or even philosophers,
to pretend to KNOW in some verbal or mathematical fashion what qualia are.
(I may send this to the list tomorrow)

Best

STAN

Gordana --

On Fri, Apr 1, 2011 at 5:04 PM, Gordana Dodig-Crnkovic
gordana.dodig-crnko...@mdh.se wrote:

I risk to discuss things above my head, but I agree with Maturana that life
and cognition coincide.

So I don’t see why would  we ascribe any cognitive functions to non-living
nature.

Cognitive is too 'rich'.  I would see {mind {cognition}}.  Cognition comes
in with the nervous system, but mind is more general, not requiring
cognition to be in effect.  So, a tree may have some manifestation of mind,
but not (seemingly!) cognition. (This example is tricky because a tree
obviously lives its life at a scale much larger than ours, and so one of its
moments might have a duration of some of our hours).

I guess that cyclone does not possess minimum of self-star properties that
we would expect from something living.

This is the main point I have been trying to insist upon so far.  Nature is
one.  The dissipative structure concept is he unifying one here.

If we would generalize qualia to organisms that do not possess nervous
system, what would that be?

I try to visualize it as what we feel in deep meditation -- no thoughts, no
emotion. No information at all.

Would plants be qualified to have qualia? Hard to imagine.

See above on the tree. I love plants, and I suppose this makes me a bit
crazy, but they do have sly behaviors.  More to the point they do have
organized chemical activities; our brains have organized chemical
activities  The organization is different, yes.  But qualia are SO
general and indiscribable ...

But cognition and even intelligence according to my understanding could be
defined without reference to subjective feeling of an organism,

and thus could be generalized to any living organism. Is that correct?

If you have an explicit model of it, then it must be able to be generalized,
by removing constraints.

STAN

Best

Gordana

Gordana --

On Sat, Apr 2, 2011 at 3:59 AM, Gordana Dodig-Crnkovic
gordana.dodig-crnko...@mdh.se wrote:

Stan,

I used my two posts in the FIS, so I reply off-list.

I continued thinking yesterday evening about what I wrote to you and I also
concluded that my skepticism about plants having qualia was not well
grounded.

I agree with you and especially concerning the fact that we have different
time scales, that human perception is  not well  attuned to recognizing such
slow and incremental changes. Plants are adaptive systems and they certainly
communicate with the world and with us. I also love plants and remember a
performance many years ago at Zagreb Musical Biennale. They connected
several plants with sensors that measured pressure, temperature and chemical
concentrations and those signals were allowed to impact on some Mozart music
piece which was played in the background.

As the public would approach the plant, Mozart music would change in
different ways, but you could hear quite quickly in fact how plant was
affected in different way as you touched them. It was a good demonstration
that plants were alive and that they obviously register inputs.

!! Wonderful!  I ```

### Re: [Fis] Discussion colophon--James Hannam. Orders and Ordering Principles

```It seems obvious to me that any property held by a very complex entity
(e.g., human being), IF it can be modeled, then that model can be used to
generalize that property ANYWHERE we wish to.  On these grounds I have been
busy working on 'physiosemiosis' using the triadic formulation of semiosis
of Charles Peirce.  I have proposed that the 'sign' emerges from the context
of an interaction between object and system.  If context has no effect on
the interaction, there is no semiosis.  If, on the contrary, context affects
the interaction, then we have semiosis, even in a pond.

The key is whether the trait involved can be modeled; on these grounds it
has not yet been shown that 'qualia' can be generalized beyond the human
experience, yet even a child can see, for example, that a mother hen is very
unhappy when her chicks are threatened.

STAN

On Fri, Apr 1, 2011 at 3:04 PM, Pridi Siregar
pridi.sire...@ibiocomputing.com wrote:

Hi all !

Maybe the term « observer » in Pedro’s « non-human observer » term is what
bugs some of you because it seems to imply some “non-human cogitum” that by
habit we may want to equate to human thinking. Of course trying to
understand the “psychology” of a bacteria may be a bit hard for humans so
perhaps the term “observer” should be given a broader meaning and the
challenge would be to define the nature/ boundaries/mechanics of this
semantic extension/redefinition. The same may hold for defining “language”
and “meaning”… But for lack of time I really haven’t followed all the
debates and I’m no philosopher.  As a business person I am much more
practical and I do have one practical concern/question: are we trying to lay
down a new theory of living systems or are we going (in some not too distant
future) towards devising a computational framework that (even modestly) may
go beyond projects such as the VHP?Sorry to be so down to earth but I
suppose that in this forum everyone is allowed to express himself/herself…
J

Pridi

*De :* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
*De la part de* joe.bren...@bluewin.ch
*Envoyé :* vendredi 1 avril 2011 19:38
*À :* l...@leydesdorff.net; 'Pedro C. Marijuan'; fis@listas.unizar.es
*Objet :* Re: [Fis] Discussion colophon--James Hannam. Orders and Ordering
Principles

Dear Pedro,

I do not quite recognize myself in the statement:

Basically, their informational subject looks like the abstract,
disembodied, non-situated, classical observer, equipped in a
Cartesian austerity --and outside, just the Order or maybe the Disorder.

I thought my implicit observer was very much real, embodied and
non-classical, fully participating (and in part constituting) the order and
disorder.

However, I rather tend to agree with you that Loet's, Rosen's and Dubois'
models of communication, anticipation, etc. are somewhat too abstract. The
models, as I think Loet may agree, are created for analysis, and do not
define the physical, dynamic relation between the models, the creation of
models and what is being modeled as processes.

I have never understood why Maturana had to say that observers are
operationally generated when it seems obvious that they exist, albeit at
different levels of complexity and (and here we agree) capability of
recursiveness. As I have said previously, autopoiesis, like spontaneity
and self-organization are concepts that are very useful, but cannot be taken
to describe, as fully as I anyway would like, the dynamics of the cognitive
processes necessary for an understanding of information and meaning.

The above notwithstanding, I then have a problem with your, Pedro,
formulation of the capabilities of non-human observers. Here, I agree with
the principle expressed by Loet that the examples of the entities you
mentioned lack the necessary cognitive abilities, although I focus on
aspects of them other than model-related.

A theory in which NOTHING previous is taken as entirely satisfactory seems
more and more necessary . . .

Best wishes,

Joseph

Ursprüngliche Nachricht
Von: l...@leydesdorff.net
Datum: 01.04.2011 12:14
An: 'Pedro C. Marijuan'pcmarijuan.i...@aragon.es,
fis@listas.unizar.es
Betreff: Re: [Fis] Discussion colophon--James Hannam. Orders and Ordering
Principles

Dear Pedro,

I understand that you have some problems with my epistemic stance. Let me
try to clarify.

Let me go back to Maturana (1978) The Biology of Language ...
On p. 49, he formulated:  ... so that the relations of neuronal activity
generated under consensual behavior become perturbations and components to
further consensual behavior, an observer is operationally generated. And
furthermore (at this same page):  ... the second-order consensual domain
that it establishes with other organisms becomes indistinguishable from a
semantic domain.

This observer (at the biological level) is able to provide meaning to the
information. ```

### [Fis] replying to James, Jerry

```As my last posting for this week:

reacting to James' fine summary --

On Thu, Mar 24, 2011 at 7:02 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

-snip-

A second, smaller camp of historians of science where I have pitched my own
tent want to know what caused modern science.  They recognise the enormous
utility of scientific discovery and seek to explain how mankind came by this
wonderful tool.

What comes to mind here devolves from the word 'tool'  The view of science
as a handmaid to technology certainly describes its present and recent past
(since the Nineteenth Century).  In my view this tool is what has allowed us
to deliver ourselves into the present seeming 'end game' of our culture.
Will this tool serve us after our primary energy sources have been
depleted?  How much of it will still be useful without massive amounts of
electricity?  Note that I am not dissing scientific inquiry per se -- e.g.,
the Galilel model of systematic curiosity for its own sake.  I am
questioning the idea that science is primarily a 'tool' for conquering the
world.

This exchange between Jerry and Steven has enlightened me about Jerry's
project, which I have not until now clearly understood.  Now I can see it as
a materialist attack upon a reputedly idealistic physicalist approach to
nature.  Can all matter be generalized to mass? I think this must depend
upon the aim of an investigation.  On this ground, I can then ask Jerry to
give us an example where using mass for all matter actually gives a

STAN

On Mon, Mar 21, 2011 at 4:55 PM, Steven Ericsson-Zenith
ste...@semeiosis.org wrote:

On Mar 15, 2011, at 7:47 PM, Jerry LR Chandler wrote:

v.547.8  Steven writes:

However, that does not avoid the fact that the universe is profoundly

uniform and it is that uniformity upon which we rely.

I disagree.

for reasoning see comment to v547.12

v547.12 Steven writes:

The universe, independent of any conception, is profoundly uniform and it
is this uniformity that is the basis of perceived universals. Our
conceptions can have no intrinsic uniformity unless they are founded upon
this profound feature of the world.

I find Steven's statement of principle to be exact.

Of, course, this line of reasoning explains virtually nothing.

With the conceptualization of mass, nature is striped of her identities.

In my view, the only intrinsic uniformity is of space and time.

The twisting of the remainder of reality to fit into the uniformity
prison, distorts  the truth of matter and the truth of matters.

This line of reasoning perfectly excluded the mental, bilogical and
chemical sciences because of the necessity for irregular extension. The
essence of the distortion of universality begins with the effort to strip
the atomic numbers of their individuality. The other consequences follow
from this antecedent.

Dear Jerry,

I elaborated on my earlier post on my blog at:

http://stevenzenith.info/the-profound-uniformity-of-the-world

I am not convinced by your contention that there is a necessity for
irregular extension that invalidates the conjecture of uniformity and ask
you to substantiate that claim.

This is not to say that there are not such extensions and that they are not
necessary for the refinement of ideas. Surely they are. But from a strictly
epistemological point of view they are indicators, pragmatic and temporary
aberrations that are ultimately resolvable by applying the necessary
uniformity conjecture.

As I note often: if a logical reduction fails it is never an indicator of
the supernatural or a justification for metaphysics. It is an indicator that
we must, of necessity, review the logical construction that failed and
ultimately revise it.

The central point of my argument is that no scientific epistemology is
possible without this conjecture of profound uniformity. If we reject it or
worse, if we find evidence that the universe is not uniform in this way, by
finding a galaxy that does not conform to the laws observed in the others
for example, then all bets are off and no scientific epistemology is
possible.

Since I take space and time to be merely a way of speaking about
mass/energy, as did Einstein, its uniformity or not is a matter of
conception alone. If you disagree then you essentially affirm the case I
make since space and time would characterize all structure in such a system
and the uniform laws and principles would be laws and principles of space
and time.

Incidentally, for me explanation is the identification of causes. The
notion of profound uniformity identifies the casual basis, the functional
dependence, of all scientific knowledge; as such it is an explanation of why
such a system works.

With respect,

Steven
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### [Fis] replies to Steven, Gary, and Jerry

```As my first posting for this week --

On Sun, Mar 13, 2011 at 6:27 PM, Steven Ericsson-Zenith
ste...@semeiosis.org wrote:

On Mar 12, 2011, at 5:52 AM, Stanley N Salthe wrote:

...

On Sun, Mar 6, 2011 at 6:46 PM, Steven Ericsson-Zenith
ste...@semeiosis.org wrote:

... I agree with that there is no knowledge outside the knower.

However, that does not avoid the fact that the universe is profoundly
uniform and it is that uniformity upon which we rely.

Well, if by 'uniformity' you mean that the results of our activities have
some predictability, I would say that what this actually refers to is that
our conceptual tools (laws, expectations, etc.) are usually successful in
aiding our projects. That is a great intellectual achievement.  But as to a
supposed actual uniformity (?statistical) of the universe, that is a product
of, and exists in, our discourses.

No, this is not what I am trying to convey.

My assertion is an existential one not an epistemological one. The universe,
independent of any conception, is profoundly uniform and it is this
uniformity that is the basis of perceived universals. Our conceptions can
have no intrinsic uniformity unless they are founded upon this profound
feature of the world.

Nor am I referring to statistical uniformity. Again, I make an existential
statement, not an epistemological one. I refer only to uniformity that
underlies the laws and principles of our observations; it is the scientific
assertion that the determinant features of the world, apprehended as laws
and principles, are everywhere the same.

This, of course, is the position of most scientists. It makes sense of their
activities.  I know of only one corroboration of this position outside of
the scientific community -- the technological / industrial /business
community -- which pays for the research.  But this really makes up only a
single intellectual community.

Then, to Steven again:

I still do not understand the appeal to postmodernism. There does not
seem to me to be anything postmodern about no knowledge outside the
knower. Indeed, it is a modern idea developed by logicians of the modern
era.

I think this view, given the obtuse attitudes of most academic scientists,
requires a label, preferably one that shocks.  Yes, this view was prefigured
by logicians, and as well, most forcefully in my view, by Jacob von
Uexküll's 'Theoretical Biology'.  In any case, most generally, the
postmodern view is anti-modern in that it eschews any supposedly universal
understanding, which modern science implicitly pretends to.  Within science,
the famous incongruity between general relativity and quantum mechanics
might have engendered a kind of postmodernism.  Instead, it has sent many
brilliant minds upon the evidently thankless task of trying to ‘square the
circle’!

I doubt your view warrants the term postmodernism for the reasons I have

Your claim that modern science implicitly pretends to a supposedly
there is an unspoken dependence then this is it.

A view that eschews any supposed universal understanding, simply cannot be
scientific. It is the view of disenchanted sociologists, philosophers or
diplomats, perhaps.

And their kinds of knowledge are to be eschewed as ... what? ... unuseful?
To what projects?  Incorrect?  Judged from what vantage point?

The profound existential uniformity that I refer to is the necessary basis
of scientific knowledge, without it all bets are off. It is certainly a
conjecture, both verifiable and fallible, but without it there can be no
science.

I think this raises the issue of what science is for.  I will suggest that
it is for the purpose of furthering technology.  That pragmatic role has
not, I think,  much value in the search for 'truth'!

As to the famous incongruity between GR and QM, each focus upon distinct
aspects of nature. Our failure, so far, to have a unified view of these
evident aspects of the world is simply an indicator that there is work to
do. If it has engendered anything it is a literal mindedness that has closed
minds to the revisions necessary and thus we have stalled. To the man with
a hammer, everything is a nail. I take it to be a warning that we must be
more rigorous, not less.

Supposing the incongruity to lie in discourse rather than in the World, then
it seems there is warrant to question the validity of these ideas.  Are they
really any better than those of disenchanted sociologists, philosophers or
diplomats?  The world of the 'small' is a mechanical (experimental)
construction, while the world of the large is a mathematical construction.  It
is true that their discourses both ride upon mathematics, and how can it be,
then, that they cannot be made to come into agreement?   Perhaps Goedel has
told us?

Incidentally, I elaborate on my earlier Science Abandons Absolute Truth
posting on my blog```

```Replying to Jerry (with implications for the postings of our Chinese
members) --

On Tue, Mar 1, 2011 at 9:43 PM, Jerry LR Chandler jerry_lr_chand...@me.com
wrote:

James Hannam, Stan, Pedro, List:

Thank you for taking the time to express your point of view.  For several
years now, I have been studying the origins of molecular biology, seeking a
coherent explanation for the meaning for its predictive powers and the
methods which lead to scientific predictions. I certainly do not speak for
the metaphysics of the physical information theorists, who, perhaps, may be

“I sense some scepticism about my contentions that ancient science could
never have developed into what we call modern science. “

is simply illogical and necessarily false.

Why do I confront your logic?

The simple facts are that the basic ideas of Aristotle remain the
foundations of Western science.  The developments from Aristotle to the
present day can be traced step-by-step.

By the basic ideas of Aristotle, I mean five specific notions that Aristotle
wrote of:

1. Rules of thought [identity, non-contradiction, excluded middle]

2. Categories [substance, quality, quantity, relation, time, place,
situation, condition, action and passion]

3. Causality [formal, material efficient, telos]

4. Logic of premises (sorites, pathways of statements from antecedents to
consequences, graph theory, theory of categories]

5. hierarchy  [individual, species, genera, alone with ostension to greater
levels]

During the intervening 23 Centuries, our notions of all these terms have
changed substantially. Our very notion of language itself, as well as our
notion of symbol systems, especially mathematics and chemistry has greatly
improved our ability to be specific. Nevertheless, modern science developed
directly from these few simple concepts, particularly of the concept of
identity. The scientific terms of Aristotle continue to serve the sciences
well and continue to be discussed routinely in both the theory and in
practice of modern science.

If Western science did not develop from these Aristotelian concepts, what
concepts did modern science develop from?

Your focus on motion, as an example, is, in my opinion, ill-advised for your
thesis. The philosophy of physics continues to churn, century after century,
it remains unsettled today. Personally, I smile a wide grin whenever a
physicist announces once again that the foundations of physics must be
revised. As one of my friends loves to say, physics is the only metaphysics
we (“modern science”) have. The other sciences, intimately associated with
the logic of calculus, thrive on the correspondence between observations and
predictions.

Is it possible, James, that your training has embedded your thinking so
deeply in the logic of language that the historical role of the logic of
calculus in the development of science is submerged in your writings?

Nice statement.  I agree with this.

Stan:

Two ideas are at issue:

1. The first is your most recent post on the role of the term, “properties.”

“There ARE NO properties of things unmediated by biology and culture.” The
concept of properties is, of course, the bedrock of predicate logic and the
grammar of physics. If you deny the existence of properties in your
ontology, your metaphysics becomes much clearer.

Clarifying more:  There can be no 'objective' knowledge of properties
outside the material abilities of the knower.  Bridgman was the most honest
physicist! And von Uexküll was the best psychologist.  There is no knowledge
outside the knower.  All is 'local knowledge' only.  Yes, this is
postmodernism.  However, even with this viewpoint as a standpoint, one can
proceed to do standard theoretical and philosophical work because, for
example, the universe IS one of our equations!  In postmodernism, scientific
theory and philosophy become artistic achievements for their own sake,
expressing humanity's, and more particularly Western Culture's imagination.
The difference, then, is that in the postmodern view, there might be other
perspectives, while in the standard scientific view there is only one true
perspective, which frequently gets locked into repressive ‘bandwagons’ (as
in Darwinian evolutionary biology, or general relativity cosmology).

1. Secondly, the notion of the term, “ostensive””.  What is it?

The Latin roots suggests the meaning

“stretch out to view”,

that is, demonstrable. In particular, are you using this term as if it is
unrelated to the concept extension that merely stretches a concept out?

I mean ‘defining by pointing to’.  It means communication unmediated by
verbal language.

STAN
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### [Fis] replies to Gavin, Guy, Jerry

```As u first for the week:

On Sun, Feb 6, 2011 at 5:04 PM, Gavin Ritz garr...@xtra.co.nz wrote:

Hi Stan

Using my last message for the week,

Reacting to the below(s):  As a materialist, I see the deformations
initiated by Guy's propagated waves (e.g., as sensations) as forming the
basis for information, but, as emphasized in semiotics, this only becomes
information (e.g. perception) as a result of assimilation by the impacted
system.

Are you saying that perception is information?

Perception is a process of making sense of sensations.  The system will not
be 'informed' by impacts that are not assimilated by it (and may not even be
sensed), and so there is no point in assigning information to sensations
(impacts) as such.

As a 'pansemiotician', I have no problem in formulating this in purely
physical systems as 'physiosemiosis', which is constructed whenever context
(in complex system this can be internal to the system) will affect the
effect of the impact.

I have no idea what this all means.

Ah, yes.  Well, semiotics is just now making its way into science. From your
point of view here, I am distinguishing Newtonian (dyadic) impacts from
interactions involving a third entity - a context.  This makes it triadic,
as in Peircean semiotics.  The impact of two entities will differ in
different contexts.  If not, then semiotics would be irrelevant.

STAN

Regards

Gavin

STAN

On Fri, Feb 4, 2011 at 7:22 PM, Gavin Ritz garr...@xtra.co.nz wrote:

Hi there Guy

I'm at a loss still about information you mention below.

If one talks about waves, light, sound these are all energy (frequency)
concepts. Chemistry and physics are really only about energy, entropy and
transduction's and conversions of energy in one form or the other of matter.

Any flows of available energy are more than likely entropy production or
free energy. (Gibbs type free energy)

The only codes, and notations are the ones we give it, it is of our own
making, if information does have an existence then its more than likely
related to non baryonic matter.

After all we are making assumptions about a universe with only a less than
4% understanding of its contents.

Regards
Gavin

Reacting to Guy's posting ...

-Original Message-
From: fis-boun...@listas.unizar.es
[mailto:fis-boun...@listas.unizar.es] On Behalf
Of Guy A Hoelzer
Sent: Saturday, 5 February 2011 1:53 p.m.
To: Foundations of Information Science Information Science
Subject: Re: [Fis] [Fwd: Re: [Fwd: Info Theory]--From John Collier

Hi Gavin,

I’m not quite sure how to respond as you didn’t ask a particular question.

Waves are indeed about energy, which I think fits nicely into the scheme I
described regarding information.  I suggested a very simple definition of
information as a contrast.  Physical gradients provide a nice example of
contrast between different conditions on either side of a gradient.  Energy
generically fits this view whether you think about it in either particle
(e.g., photon) or wave form.  I am not a physicist, but I think energy
always exists as some sort of localized concentration with a gradient
between regions of higher energy and regions of lower energy.  In this
sense, energy can always be considered as a spatially configured pattern,
and thus as information.

So here you seem ready to invoke Bateson's 'difference that makes a
difference'. But I don't see here the system for which this difference is
made.  On my own definition of information -- any constraint on entropy
production -- I don't see that here either.  Shannon's view of information
as a reduction in uncertainty might be implicit because without any
constraints the system will rapidly go to local equilibrium. In all three of
these views of information an observing or participating system is implicit.

I also agree that flows are about entropy production, and they must always
be channeled in a way that requires a structural configuration.   This is
how I think about self-organizing dissipative systems.  Flows cross
contrast and thus the amount of information exhibited by the gradient.  I
would describe the emergent structure of such systems as information
captured by the system, or transferred to the system, as the gradient is
diminished.

An intriguing suggestion.

I see this as an alternative way to say that the system captures free
energy from the flow and uses it to construct itself.  I generally see
information as the inverse of entropy, so the existence of information goes
hand-in-hand with the existence of entropy.  Whether information/entropy
exist or are just heuristic concepts is an issue for others to debate.  I do
think, though, that it IS related to baryonic matter.

Agreed on all of these.

Stan:

The issue of ostension remains high on my agenda. The individual sciences
progress along individual ```

### Re: [Fis] On Stan's reply to Gavin

```Robin --

On Mon, Jan 31, 2011 at 7:42 AM, Robin Faichney ro...@robinfaichney.orgwrote:

Saturday, January 29, 2011, 9:39:09 PM, Stanley wrote:

On Mon, Jan 24, 2011 at 6:41 AM, Gavin Ritz garr...@xtra.co.nz wrote:

SS: Info theory presumably applies to everything and anything.

GR: It was never intended to apply to anything but communication
instruments. That is sending English language down a pipe.

S: Since it was abstracted from human communication systems, it has
taken on a 'life of its own', as any abstraction has a right to do.

I   agree   with   this.  I'm no mathematician, but I believe that the
broader  significance  of  Shannon's  work was a method of quantifying
pure  pattern.  This  was  then  adopted  by physicists who saw that
material  form  can  be treated as pure patterns, and thus we get such
concepts as the conservation of information in quantum mechanics and
in  black  holes.

Are 'pure patterns' three dimensional?

Conservation  of information can be translated as
meaning   that   physical   laws  do  not break down, and the state of
affairs  at  one  time  can  be  considered  encoded in the state of
affairs at another time. For instance, events within the event horizon
of  a  black hole (or, on the holographic principle, on the surface of
the  event  horizon) could, in principle, be determined by examination
of the Hawking radiation that escapes as the hole diminishes.

Nice, clearly put!  Thanks.  Of course, this is a (necessary!) assumption.

I think
the crux of the matter is being examined right now -- is information
('bit') primal or is stuff ('it') primal?  In my view there needs to
be stuff in order for there to be a perspective, and there needs to
be a perspective before there is anything to communicate.

I  share  your  focus  on  perspective (and also context), but I'm not
clear why perspective requires stuff -- but see below.

Because a perspective would require stability of locale.  I think that a
world of boson-fermion transitions could have no specific locales.

Information is an abstraction related closely to form, which it is
supposed always could be translated to instructions in a computer,
creating 'bits' from inspection of 'its'.  Then the supposition is
that The World also reckons with information, leading to 'its from
'bits' .  This, to me, is implausible.

I tend to feel the same way about it from bit, but I think it should
perhaps  be  taken as implying that the idea of substance derives from
form,  which to me is highly plausible.

So, form here is potentiality.  But where could this come from without
some constraints?

We can take the view that form
is  what  we encounter -- at all levels, personally and scientifically
--  and  substance  a  theoretical entity or set of such. This view is
related  to  philosophical  idealism,  and  is,  like that, I believe,
strictly irrefutable. By the same token, being unverifiable, it has no
practical  consequences. Which is more real, or which came first, form
or substance? These questions are, strictly speaking, meaningless.

In a 'logical' sense, yes.  But metaphysics transcends logic, and treats of
its preconditions as well.  On 'verifiability', I'm afraid I have been
influenced by the Duhem-Quine thesis.

Etymologically,  information is extremely closely related to form,

Strongly agree. Its function then is to constrain entropy production.

and  the  concept  of  information  used in physics simply IS material
form,  where  that is generalised from shape to encompass all material
properties.  Just as past and future states of affairs are encoded in
the  present,

I suppose this takes into account historicity?  Via statistics?

so  genetic  information  is encoded in DNA. Biological
information  is  just a subset of physical information. DNA molecules,
like  all  physical  entities,  encode  the  outcomes  of all of their
potential  interactions,  but  in  the  case  of  DNA the outcomes are
constrained by the cellular context.

But we now know that there is a good deal of material manipulation and
modification in between DNA code and protein complexes.  You could say that
the DNA information is generic, while what emerges from metabolism is
particular.

I'm  currently  working  on  a paper in which I argue that intentional
information   --   using   intentional   in  Brentano's  sense,  and
encompassing  meaning  and  all  mental  content -- is best considered
encoded  in  physical/biological  information,  being  decoded in use.

But the DNA stuff is generic, use is particular.

Perspective is obviously highly relevant here, but it seems to me that
it  can  probably  be  explained  in  (literally)  formal  terms, that
substance  as such need not enter the picture, but perhaps I'm missing
something?

As I said above, I don't see how there can be other than material
persectives, because only matter is 'sticky' enough ```

### [Fis] Replies to Gavin Jerry

```Gavin --  I send this reply to you, but, since we on this list are allowed
only two messages per week, I will reserve sending it to the list until
later in the week.

On Mon, Jan 24, 2011 at 6:41 AM, Gavin Ritz garr...@xtra.co.nz wrote:

Hi there Stan

SS: Info theory presumably applies to everything and anything.

GR: It was never intended to apply to anything but communication
instruments. That is sending English language down a pipe.

S: Since it was abstracted from human communication systems, it has taken on
a 'life of its own', as any abstraction has a right to do.

GR: In my opinion it still only does, I cant get my head around how say
information theory actually applies to direct human communication or organic
sensing systems.  All our sensing systems are energy transduction systems,
once inside the individual it 's moved via Na/K pumps aided by ADP to ATP
conversions to the brain all electrical, chemical energy. So in the
environment it's just a sound (phonon) or light (photon) or chemical or heat
energy where are the bits (information theory part) or markers. They are
just not there.

Unless this information is what underlies energy and is what makes up the
rest of the universe including dark matter and dark energy. And is also what
underlies the theory of Geometricdynamics.(Relativity theory)..?? How so
I would not know.

S: As a materialist, I have sympathy with your view here.  I think the crux
of the matter is being examined right now -- is information ('bit') primal
or is stuff ('it') primal?  In my view there needs to be stuff in order for
there to be a perspective, and there needs to be a perspective before there
is anything to communicate.  But, given this, I go further and argue that
semiosis (as physiosemiosis) emerges simultaneously. I define semiosis as
reaction mediated by context.  Any perspective will have a context, and IF
that context has an effect on a locale's reaction (i.e., acts as a sign),
then that is ( at least proto) semiosis.  So:

Big Bang -- matter -- locales -- contextuality -- semiosis

On this view the Newtonian action -- reaction is a debased, if not wholly
fictional construction.  Concerning 'dark things', in my view they are
mathematical variables.

STAN

Gavin --

On Mon, Jan 24, 2011 at 7:50 PM, Gavin Ritz garr...@xtra.co.nz wrote:

Sure it can have a life on its own, but fundamentally human communication is
the integration of (sound) phonons and sight (photons) that is vibration of
matter across a wide frequency spectrum. There's no information there? I see
only energy. Language in my opinion is matter's desire to be be known.

Information is an abstraction related closely to form, which it is supposed
always could be translated to instructions in a computer, creating 'bits'
from inspection of 'its'.  Then the supposition is that The World also
reckons with information, leading to 'its from 'bits' .  This, to me, is
implausible.

STAN

On Mon, Jan 24, 2011 at 5:05 PM, Jerry LR Chandler jerry_lr_chand...@me.com
wrote:

List:

My responses to recent posts by Karl, Stan, Joe, Loet, Gavin, John, and Bob
by the number of the digest that I rec’d. I seek to address several basic
issues.

-snip-

Stan (545:10) *Re: [Fis] Ostension and the Chemical / Molecular Biological
Science*,   …It is this translation from material observations into logical
form, in particular into fully explicit, crisp logical form that I am
questioning.  Yes, it can lead to short term triumphs, via engineering,…

JLRC: Hu, I think you miss the point. The abstract symbol systems of
Dalton, Lavoisier, and Coulomb underly the foundations of thermodynamics as
well as the Shannon theory of information as well as our concept of such
abstractions as “energy” and “entropy.” These symbol systems are now firmly
embedded in the logic of scientific communications. Perhaps you wish to
infer that concept of ostension is not useful in the natural sciences?  Or,
is it that in your world view, “utility” is a bad word?

Actually, yes, 'utility' IS a bad word in my view.  We have virtually
wrecked the world basing our actions almost solely on utility.  Peirce's
pragmaticism is a broader and philosophically more sophisticated notion than
pragmatism.  Then, The abstractions of physical science, deployed using
maths, have certainly been useful in the unfortunate ascendency of our
culture. Their use in natural settings is limited to (admittedly powerful)
generalities, as opposed to their detailed uses in engineered experiments.
They cannot be used to deal accurately with unforeseen and unforeseeable
contexts, which history continually generates in the world.  That said, I
greatly admire thermodynamics when deployed generally in philosophical
inquiry because it does relate to sensible general properties of the world
useful for understanding (as opposed to exploitation).

BTW, Lavoisier / Daltonian logical forms are not fully explicit in the usual
sense of ```

### Re: [Fis] Future discussions

```Tagging on after Joseph --

On Tue, Jan 18, 2011 at 9:19 PM, joe.bren...@bluewin.ch
joe.bren...@bluewin.ch wrote:

Dear Pedro and All,

Thank you for your note and the ambitious program. My brief comments by
theme:

--Theme 1: Historical Foundations of Modern Science.

Sounds very interesting; the Science and Society aspect fits well with
Theme 3.

I hope it will discuss how science was taken over as (became limited to)
support for technology.

-- Theme 2: On Information Theory.

My hope is that this discussion will have a good deal to do with
qualitative as well as quantitative aspects of information. Perhaps people
should state clearly what the primary interests and objectives are of their
remarks.

Maybe it could take up ostension?  This would bring in vagueness (or at
least fuzzy information theory)?

-- Theme 3: Foundations of Social Information Science.

This should be a fascinating occasion to evaluate different social models
from an informational standpoint.

Again, ostensible communication. Pointed absence of communication?

STAN

Cheers,

Joseph

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### Re: [Fis] reply to Javorsky. Plea for (responsible) trialism

```One of the most special properties of science -- indeed its core that
differentiates it from natural philosophy -- is the practice of testing
hypotheses.  Leaving aside the 'human' weaknesses involved here, there is,
however, the 'Duhem-Quine thesis' to be faced.  In order to test an
hypothesis, one must rig up some more or less elaborate set-up. This
involves various ancillary  assumptions, and even other hypotheses, that
enable the test, but that are not being tested themselves.  A failure to
corroborate an hypothesis does not automatically lead to rejection, because
some of these ancillary assumptions may have been inappropriate.  And so on.
No single failure to corroborate can impugn an hypothesis, but the question
even is -- 'can anything at all be tested adequately?'.

This need not slow down a science.  For example take evolutionary biology
and its key hypothesis that natural selection is the mode by which
macroevolution (e.g., ape - human) occurs.  Natural selection has been
tested adequately, and shown to operate to preserve the adaptedness of a
population, from one generation to the next.  But its application to
macroevolution has been testable (?) only in laboratory populations of
microorganisms.  Nevertheless natural selection remains the key ASSUMPTION
of all evolutionary thinking. Its role in macroevolution is NOT testable,
but is used to organize a major research program on the basis of its
plausibility.

STAN

On Thu, Jan 6, 2011 at 1:09 PM, Loet Leydesdorff l...@leydesdorff.netwrote:

Dear John and colleagues,

The idea that the rationality of science is in the specifics of its nature
as an institution goes back at least to C.S. Peirce, and does not lie in the
activities or reasoning of specific scientists. The the sociological
approach misses the target completely, and is rather mundane and relatively
uninteresting (to use Jim Brown's words). Science is, indeed, just another
institution, but it has rather special properties that are missed when we
focus on the activities and rationales of individuals within the
institution.

I would maintain that both the institutions and the individuals reflect
developments in the communication of science at the global level. Thus they
participate insofar as the communication can be understood and brought
forward (reproduced and changed). The codes of communication are specific;
to universities during the 19th century. Of course, institutions can last
longer than  individuals.

I am not pleading against ethnography and other forms of sociology of
science. However, the core subject is our subject: how is scientific
information communicated? And how is this communication system (including
scholarly discourses) evolving? The study of institutions provides us with
windows of instantiations which can be interesting in themselves (for
example, national differences).

Best wishes for a happy New Year,

Loet

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### Re: [Fis] Replies to Walter Loet

```Replying to Loet --

On Sun, Dec 19, 2010 at 1:59 AM, Loet Leydesdorff l...@leydesdorff.netwrote:

Your distinction between the backward looking institutional viewpoint
and the forward looking evolutionary perspective is cogent, but it plays
down the fact that the evolutionary one is restrained by current hegemonies
of theory and interpretation, always linking new discoveries to the
already-accepted 'facts'.  So, I think that, for example, the parcelling of
energy expenditures between these viewpoints is rather something like 80%
institutional (including education in discovery techniques} and 20%
evolutionary.

Dear Stan,

In my opinion, this is the crucial parameter for measuring the extent to
which a system has become knowledge-based. In a previous (for example,
political) economy, the institutions can be expected to leave less room for
the knowledge-based (sub)dynamics than in a knowledge-based economy. The
latter reinforce the restructuring from the perspective of what is possible
given the models. The models open up possibilities and thus the redundancy
within the system can be increased.

Original Stan: But all knowledge must in the end be a 'building upon'
previous knowledge.  On this account knowledge that implies completion, or
which is too detailed, will lead nowhere, for it leaves nothing left to do
but follow the institution. There has been a discussion of 'evolvability' in
the complexity sciences that relates to this issue.  From my own development
theory, we can see that continued development of a system leads to
increasingly trivial additions to an ascendent discourse ('normal science'),
a filling in of details.  This leads eventually to overthr

Best wishes,

Loet

Then,

I would say that there is a third major kind of information -- information
as constraint (on anything, therefore on entropy production).  This comes
out of Pattee's distinction between dynamics and non-holonomic constrain.
Example: examine an equation, say simply Y = aX^b.   a and b are
functioning as information here.  This information is not uncertainty, and
it does not overtly imply an observer in the usual sense.  If we generalize
the observer, it might be said that a and b make a difference to ... ? ...

STAN

On Mon, Dec 20, 2010 at 11:31 AM, Loet Leydesdorff l...@leydesdorff.net
wrote:

Information is the difference that makes the difference

Dear colleagues,

It seems important to me to distinguish between two concepts of information
because if we use the same word for two concepts this can be a source of
confusion. Perhaps, I can reproduce the two character set in Chinese which
Prof. Wu Yishan was once so kind to write for me in Chinese and which
express these two meanings. Let me give it a try:

Description: fig13_01

The above one, ‘sjin sji’, corresponds to the mathe matical definition of
informa tion as uncertainty.[1] The sec ond, ‘tsjin bao,’ means infor mation
but also intelligence.[2] In other words, it means infor mation which
informs us, and which is thus considered meaningful.

-snip-

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### [Fis] Replies to Walter Loet

```As my last for this week:

Replying to Walter --  The dark matter and dark energy examples are not very
strong as examples of demonstrating discoveries rather than invention!
These are stand-ins, just names, for disparities between predictions and
observations.  They are provisionally (I hope!) accepted because they fit
into the current 'standard model'.  In my view, a much neater way to solve
the disparity leading to the dark matter idea would be too accept that the
gravitation constant, g, is not constant everywhere or at al times.  But
that would not fit well into the Standard Model, and would impair the
ability to do certain calculations because one needs some constants in order
to solve equations.

who replies:

Stan,

Your notes help me to make my point much clear, thanks.

These cases are not truly adequate, I accept that, but they would if they
were actually confirmed.

What I wanted to refer to is about the power of conditionals:

“If dark matter and dark energy are not provisional, but becomes highly
confirmed then the Standard Model needs important revisions”

And also, I wanted to draw attention to the conceptual changes:

- One interesting example is the discovery that speed of light is a
fundamental constant of the universe and its impact in the way it produces a
change (from Newtonian to Relativity theories).

- The case of second law of thermodynamics in times of Maxwell is an
interesting one.

- Another is the case in times of Kepler: his elliptical orbits and the
conflict with the more accepted celestial circularity

I guess this capacity is inherent in science (to be open to changes
fundamentally by the discovery of new facts) it is certainly not the case in
other human activity.

Sincerely,

Walter

ORIGINAL MESSAGE:

On Sun, Dec 12, 2010 at 8:10 PM, walter.riof...@terra.com.pe wrote:

Dear Loet, Stan, Pedro, colleagues,

In these topics there are a number of different approaches but the central
issue is referred to on what could be a science (or a scientific discourse)
and what is not (and what are the criteria to discern between them).

In the human world we have many activities: ordinary activities, political
activities, sportive activities, religious activities, hobby activities,
and…..academic activities (one of them is the scientific activity).

It would be a “great confusion” (to say the least) display all the behaviors
associated with the religious activities in, for instance, a tennis match…

Accordingly, we have certain preliminary criteria that you are taking into
account in your notes --some internalist and some externalist--, referred to
the human scientific activity.

Our scientific products are “just stories” or “narratives”, equivalent to
the story about himself of a storyteller in the Nobel Banquet?

I suppose that many (if not all) of us have diverse reasons to answer with a
resounding negative response.

Although we can say that as all the other human activities that are also
constrained by our capacities and limitations, the scientific (and
philosophical) activities have the advantage that its products are under the
public scrutiny of people with very high academic abilities (and maybe with
a methodological skeptic view).

These people look at the rationale of the proposals and/or results of
scientific products and its consequences in reality.

The scientific activities aim to increase our knowledge of nature and about
ourselves --or I suppose that it is the ideal.

For instance, nobody could know around 1998 that almost five percent of the
universe is matter and energy and the rest something that we now call as
dark-matter and dark-energy…

How these *facts* would affect our theories and knowledge in physics and
chemistry?

What could be nowadays the epistemological and metaphysical status of “The
Universal”?

It seems that these kinds of questions not arise in other human activities…I
think…

Sincerely,

Walter

--

Replying to Loet --  I will post this to fis later in the week

Your distinction between the backward looking institutional viewpoint
and the forward looking evolutionary perspective is cogent, but it plays
down the fact that the evolutionary one is restrained by current hegemonies
of theory and interpretation, always linking new discoveries to the
already-accepted 'facts'.  So, I think that, for example, the parcelling of
energi expenditures between these viewpoints is rather something like 80%
institutional (including education in discovery techniques} and 20%
evolutionary.

On Mon, Dec 13, 2010 at 4:20 AM, Loet Leydesdorff l...@leydesdorff.net
wrote:

Dear Stan and colleagues,

I agree with Joseph Brenner that we need both, but the status of the two
theories is different. Behavior of agents (scholars) and relations among
texts can be mapped. In this case, we use a theory of the measurement and
focus on the retention mechanism of the evolving science system. At ```

### Re: [Fis] reply to Javorsky. Plea for (responsible) dualism

```in my first for the week, Replying to Joseph:

Dealing as I do with hierarchies and thermodynamics, I have come to the
postmodern conclusion that our explicit scientific knowledge is a logical
construct -- unlike our intuitive 'knowledge' (viz. qualia) of the world we
are IMMERSED IN.  In these scientifically-based efforts we create a logical
simulacrum (which I call 'Nature') of The World.  Its basis is logic and
esthetic, but today it also passes through a pragmatic filter imposed by
those who pay for the science.  This latter bias works mostly in choice of
study objects.  Stepping back from active engagement in the process of
gaining primary knowledge in these ways, I feel that I am these days
engaging in a renewed Natural Philosophy -- an attempt to construct a
scientifically based 'mythology' for moderns, meant as an alternative to
religious myths.  These latter importantly have also engaged, via rituals,
the qualia we are immersed in.  Inasmuch as Natural Philosophy has no such
practices associated with it, the primary function of the emerging Nature is
to challenge the religiously based myths associated with the rituals in an
attempt to unseat the associated political establishments (Rome, the
Caliphate, the Republican Party, etc.) that enforce them.

On Thu, Dec 9, 2010 at 7:54 AM, Joseph Brenner joe.bren...@bluewin.chwrote:

Dear All,

In agreeing with Bob, I would like to point out that his critique is not
theoretical philosophy. He is calling attention to something essential
missing in the pictures and models of Stan and Karl, namely, 1) the life
and blood of the world; 2) that that life and blood follows different
rules than the entities in the models; 3) those rules are based on real
dualities of equal ontological purport: order and disorder, continuity and
discontinuity, entropy and negentropy; etc.; and 4) these dualities play
out in real interactions in biology, cognition and society, for example
in information and non-information.

It is perfectly possible to see grids of numbers and levels or
hierarchies
in Nature as abstract structures - this is indeed Karl's word, as is his
use
of independence - but this is not going toward the world, but away from
it. The world includes Karls and Stans and Josephs and Bobs, and I
challenge
anyone to propose a theory that insures that our antagonisms, which are
real, also receive some logical treatment.

I for one do not know everything  about everything I'm made of (cf. our
fluctuon discussion), but I have the feeling it is not abstractions or
sequences of numbers. I mentioned string theory, but I am by no
means pushing it as the full story.

Cheers,

Joseph

- Original Message -
From: Robert Ulanowicz u...@umces.edu
To: fis@listas.unizar.es
Sent: Friday, December 03, 2010 4:52 PM
Subject: Re: [Fis] reply to Javorsky

Dear All:

At the risk of being seen as the one who tries to throw a monkey
wrench into the fine discussion you all are having, I would like to
among monist scenarios.

I see the world as dual, not in the sense of Descartes, but of
Heraclitus. If I am correct, then any strategy predicated on a monist
principle is destined to lead to disaster. (Stan and I have gone round
and round on this. I see entropy as double-sided and not simply as
disorder. [Ecological Modelling 220 (2009) 1886-1892].)

But I'm hardly the only one to warn against a monist view. Terry
Deacon's model of self-organization, the Autocell acts similarly.
The process starts by using up external gradients as quickly as
possible, but gradually shuts down as the autocell nears
self-completion. (Deacon, T.W. and J. Sherman. 2008. The Pattern Which
Connects Pleroma to Creatura: The Autocell Bridge from Physics to
Life. Biosemiotics 2:59-76.)

The best to all,
Bob

-
Robert E. Ulanowicz|  Tel: +1-352-378-7355
Arthur R. Marshall Laboratory  |  FAX: +1-352-392-3704
Department of Biology  |  Emeritus, Chesapeake Biol. Lab
Bartram Hall 110   |  University of Maryland
University of Florida  |  Email u...@cbl.umces.edu
Gainesville, FL 32611-8525 USA |  Web http://www.cbl.umces.edu/~ulan
--

Quoting Stanley N Salthe ssal...@binghamton.edu:

one can use a stable model used by neurology and psychology to come
closer
to understanding how our brain works. This can help to formulate the
thoughts Pedro mentioned being obscure.

One pictures the brain as a quasi-meteorological model of an extended
world
containing among others swamp, savanna, arid zones. The dissipation of
water
above these regions causes clouds to form and storms to discharge the
vapor
within the clouds. The model observes```

```*Replying to Karl, who said:*

one can use a stable model used by neurology and psychology to come closer
to understanding how our brain works. This can help to formulate the
thoughts Pedro mentioned being obscure.

One pictures the brain as a quasi-meteorological model of an extended world
containing among others swamp, savanna, arid zones. The dissipation of water
above these regions causes clouds to form and storms to discharge the vapor
within the clouds. The model observes the lightnings in the model and sets
them as an allegory to thoughts (these being electrical discharges) as
opposed to hormones (that are the fluids in the swamps). So there is an
assumed independence between the rainfall, the humidity of the ground, cloud
formation and lightnings. The real meteorologists would not agree with the
simplification that the lightning is the central idea of a rainfall, but
this is how the picture works (at present).

Why I offer these idle thoughts from the biologic sciences to FIS is that it
is now possible to make a model of these processes in an abstract, logical
fashion. The colleaugues in Fis are scientists in the rational tradition and
may find useful that a rational algorithm can be shown to allow simulating
the little tricks Nature appears to use.

Nature changes the form of the imbalance, once too many or too few
lightnings, once too much or lacking water - relative to the other
representation's stable state. There are TWO sets of reference. The
deviation between the two sets of references is what Nature uses in its
manifold activities.

This model looks at the physical equivalences in two realms by
modeling in thermodynamics.  Today in thermodynamics we have an advancing
perspective known as the ‘Maximum Entropy Production Principle’ (MEPP) for
relatively simple systems like weather, or Maximum Energy Dispersal
Principle’ (MEDP) for complicated material systems like the brain.  In both
cases the dynamics are controlled by the Second Law of Thermodynamics, which
imposes that the available energy gradients will be dissipated in the least
possible time, taking the easiest routes available.  This becomes very
interesting in the brain, where the flow of depolarizations would then be
predicted to be biased in the direction of more habitual ‘thoughts’.  I
think that this prediction seems to be born out in our own experiences of
the frequent return of our attention to various insistent thoughts.  I
recommend that Karl inquire into MEPP.  For this purpose I paste in some
references.

STAN

MEPP related publications:

Annila, A. and S.N. Salthe, 2009.  Economies evolve by energy dispersal.
Entropy, 2009, 11: 606-633.

Annila, A. and S.N. Salthe, 2010. Physical foundations of evolutionary
theory. Journal on Non-Equilibrium Thermodynamics 35: 301-321.

Annila, A. and S.N. Salthe, 2010.  Cultural naturalism.  Entropy, 2010, 12:
1325-1352.

Bejan, A. and S. Lorente, 2010.  The constructal law of design and evolution
in nature. Philosophical Transactions of the Royal Society, B, 365:
1335-1347.

Brooks, D.R. and E.O. Wiley, 1988. Evolution As Entropy: Toward A Unified
Theory Of Biology (2nd. ed.) Chicago. University of Chicago Press.

Chaisson, E.J., 2008.  Long-term global heating from energy usage.  Eos,
Transactions of the American Geophysical Union 89: 353-255.

DeLong, J.P., J.G. Okie, M.E. Moses, R.M. Sibly and J.H. Brown, 2010. Shifts
in metabolic scaling, production, and efficiency across major evolutionary
transitions of life. Proceedings of the Natiional Academy of Sciences. Early
EDition

Dewar, R. C., 2003.  Information theory explanation of the fluctuation
theorem, maximum entropy production, and self-organized criticality in
non-equilibrium stationary states.  Journal of Physics, A  Mathematics and
General 36: L631-L641.

Dewar, R.C., 2005.  Maximum entropy production and the fluctuation theorem.
Journal of Physics A Mathematics and General 38: L371-L381.

Dewar, R.C., 2009.  Maximum entropy production as an inference algorithm
that translates physical assumptions into macroscopic predictions: Don't
shoot the messenger.  Entropy 2009. 11: 931-944.

Dewar. R.C. and A. Porté, 2008.  Statistical mechanics unifies different
ecological patterns. Journal of Theoretical Biology 251:389-403.

Dyke, J. and A. Kleidon. 2010. The maximum entropy production principle: its
theoretical foundations and applications to the Earth system.  Entropy 2010,
12:613-630.

Herrmann-Pillath, C., 2010.  Entropy, function and evolution: naturalizing
Peircean semiosis.  Entropy 2010, 12: 197-242.

Kleidon, A. (2009): Non-equilibrium Thermodynamics and Maximum Entropy
Production in the Earth System: Applications and Implications,
Naturwissenschaften 96: 653-677.

Kleidon, A. (2010): Non-equilibrium Thermodynamics, Maximum Entropy
Production and Earth-system evolution, Philosophical Transactions of the
Royal Society A, 368: 181-196.

Kleidon, A. and R. Lorenz (eds) Non-equilibrium Thermodynamics ```

### [Fis] replies to Walter, loet Joseph

```Replying to Walter --

On Fri, Nov 26, 2010 at 8:41 PM, walter.riof...@terra.com.pe wrote:

Dear Colleagues,

It seems that a good start point is to look at the “dissipative structures
world”.

And we could ask if in every dissipative structure it is possible to find
information

and/or computations and/or intelligence and/or the like…

Of course no in cyclones and hurricanes, neither in Bénard cells and
Belousov-Zhabotinsky reactions, but we would almost surely affirm the living
systems have these capacities.

At least, we can affirm it would be in animals and plants, but in archaea
and bacteria?

Keep in mind that these microorganisms usually exist in multispecies
communities,like biofilms.  This makes them more less equivalent to simple
living tissues.

or, in prebiotic systems?

As an evolutionist and materialist, I would expect that any property
higher living forms have would have had precursors in more primitive,
ancestral systems -- but, of course in more rudimentary form.

My bet is that there was a beginning from which we could talk about
information (with meaning)

and then, on natural computations and then, on behaviors and then, on
cognitive phenomena and then, on other more sophisticated phenomena and so
on…

This beginning was the one with “minimal complexity”.

A kind of molecular dissipative structure with processes behaving like
dynamic biological constraints: (1) a container made of amphiphilic
molecules and (2) a micro cycle, driving the protocell far away from
thermodynamic equilibrium, and with the basic properties of life: biological
information and biological functions…and then, we could talk on autonomous
agents…(Riofrio 2007).

Could I have copy of this?  Thanks.

Nowadays, comparative genomics, metagenomics and system biology are
increasingly showing that natural selection is only one of the forces that
shape evolution, and even it is not quantitatively dominant. It happens that
non-adaptive processes are much more prominent than previously thought
(Kelley  Scott 2008; Koonin  Wolf 2009; Dhar  Giuliani 2010; Doolittle
Zhaxybayeva 2010).

Perhaps, more than one of these forces shaped evolution before Darwinian
threshold was reached by protocells.

Some think that self-organizing forces predominate in ontogenetic
development, and may be responsible to discovering new forms.

And this circumstance is owed to the fact that each new level of complexity
materializing in the universe implies, by necessity, the emergence of new
properties containing causal efficacy that will, in the end, produce new
events in our universe.

Moreover, we contend this prebiotic world might have been comprised by an
almost continuous series of systems, and when we talk about continuous, it
is in the sense that the most fundamental properties of these different
types of systems – behaving as the details of a specific, self-organizing
kind – would have been shared by all of them.

In consequence, it is possible that these molecular dynamics had provided
the conditions for the emergence of the first small world structures as core
characteristics to the way in which the biological realm computes.

That looks promising.

Sincerely,

Walter

On Sat, Nov 27, 2010 at 2:41 AM, Loet Leydesdorff l...@leydesdorff.net
wrote:

Dear Stan,

It seems to me that “senescence” applies to system components which are
continuously replaced (generationally) by the autopoietic or dissipative
system, while the system at this next-order level can be expected continue
to develop (or stagnate).

For example, the clouds come and go, but the weather pattern is continued.
Of course, a systems level can itself be embedded in a next-order system and
thus be replaced, but at a much lower frequency level.

Yes, I would propose that all dissipative systems follow the 'canonical
developmental trajectory' shown in my posting.  So, what you say here could
be the case.  The 'next-order level' would itself necessarily senesce
eventually, but at a much slower rate.

Thus, we have to distinguish in terms of the vertical levels of the
hierarchy. J

As you know, this is of great interest to me!

**Then, replying to Joseph, who said:

One of the important aspects of Pedro's limitations as that they
themselves appear to me, at least, to be the resultant, the effect of some
kind of interactions, as well as have causal power for further development.
Thus Stan is

right in calling attention to senescence, but anti-senescence also
exists and the 2nd Law alone (massive input of energy) is necessary but not
sufficient to explain it.

Anti-senescence is reproduction of new dissipative structures, as in weather
systems and living systems.  My point is that tis is the usual focus of
almost everyone in our growth-fascinated culture, while senescence is almost
always avoided as a topic of inquiry, except in medical circles.  As our
global society ```

### [Fis] Fwd: Doctrine of Limitation

```As my second posting for the week:

-- Forwarded message --
From: Stanley N Salthe ssal...@binghamton.edu
Date: Fri, Nov 26, 2010 at 9:47 AM
Subject: Re: [Fis] Doctrine of Limitation
To: Pedro C. Marijuan pcmarijuan.i...@aragon.es

Optimality principles can be discussed now, but limitation may be
easier. Why the cell, any cell, does not grow indefinitely its genome
(stock of knowledge) so to indefinitely increase its repertoire of
intelligent mechanisms? Why the proteins encoded in bacterial genomes,
the intracellular intelligent components or molecular agents, are not
far bigger and powerful? And why do they become substantially smaller
than their eukaryotic counterparts? Limitations of genome size, of
energetics of protein synthesis, and those due to the folding process
(problem) have to be invoked, among others.

I like to point out a limitation that faces all dissipative structures --
senescence.  Here again is the scheme:
---

IMMATURE STAGE

Relatively high energy density (per unit mass) flow rate

Relatively small size and/or gross mattergy throughput

Rate of acquisition of informational constraints relatively high, along
with high growth rate

Internal stability relatively low (it is changing fast), but dynamical
stability (persistence) is high

Homeorhetic stability to same-scale perturbations relatively high

MATURE STAGE (only in relatively very stable systems)

Declining energy density flow rate is still sufficient for recovery
from perturbations

Size and gross throughput is typical for the kind of system

Form is definitive for the kind of system

Internal stability adequate for system persistence

Homeostatic stability to same-scale perturbations adequate for recovery

SENESCENT STAGE

Energy density flow rate gradually dropping below functional
requirements

Gross mattergy throughput high but its increase is decelerating

Form increasingly accumulates deforming marks as a result of
encounters, as part of individuation

Internal stability of system becoming high to the point of
inflexibility

Homeostatic stability to same-scale perturbations declining

TABLE 1: Thermodynamic and informational criteria of the developmental
stages of dissipative structures. See Salthe (1989, 1993) for more details
and citations.

---
Combining this with the limitations on length of life and the Darwinian
postulate about the urgency to reproduce more rapidly than others in a
population, we can generate an argument that there would be no point to
elaboration beyond some basic minimum.  This is advanced upon the notion
that the purpose of living forms is simply to reproduce.

Adding to this general point, I would also cite a paper in *Science* (330:
920-921) 2010: Irremedial Complexity by Gray et al, which posits that cell
machinery -- like a Rube Goldberg machine -- is much more complicated than
it needs to be to perform its functions.

The more complicated a system is, the more there is that can go wrong.  This
principle adds to the senescence argument, urging that systems stay simple,
live fast, and die a multiple parent.

STAN

On Fri, Nov 26, 2010 at 8:05 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Dear FISers,

Thanks to Christophe for his agents narrative and to Joseph for openly
buying populational thinking and the doctrine of limitation. As for
the narrative, I concur that the link between intelligence and info
implies the introduction of some agent thinking --what kind of agent
and scenario? Krassimir has attempted here some general-style option
too. Murray Gell-Mann framed an interesting general description, about
Information Gatherers and Information Utilizers or Iguses (in the
Quark and the Jaguar, 1995), which was accepted by quite many
complexity scientists afterwards. The point is that knowledge gets
introduced into a workable conceptual scheme together with information
and intelligence.

Let me try a different track. Starting with an ample conception of
intelligence, for instance what Raquel and Jorge penned the capability
to process information for the purpose of adaptation or problem solving
activities. In the case of cells, problems can be caused by the
environment, extracellular aggressions, communications, etc. But an
important aspect is missing here. If we see some biological entity
regularly entering some metabolic inputs and processing some external
signals, we do not get much attracted to ad the term intelligence
(plants, for instance). Rather intelligence implies the ability to
manipulate the life stories (and evolution) of the living portions of
the environment and to develop efficient mechanisms (for
cooperation/defence/aggresion) conducing to survival and
multiplication.  The important difference is the introduction of the
life cycle concept, either as life stories```

### Re: [Fis] fis Digest, Vol 543, Issue 19 (John Collier) and footnote to fluctuon discussion (Stanley N Salthe)

``` being involved.  If
such would occur during neuron cycling in one cell, it would again be
swamped out at the levels of networks, or maps or higher systems. If one got
promoted to the level of consciousness, it might be experienced fleetingly
for the moment, then forgotten.

The scientific facts support the conclusion that the reflexivity of a
human being is an emergent property of life, not mathe-magic or philo-magic.

Reflexivity of a human being seems like something more than the above
definition.  Experience may have a cumulative effect, of course, especially
if repeated, but none of it would, I think, be acquired by fluctuation in a
neuron (which would be non-repeatable).

STAN

Cheers

Jerry, forever the realist.

On Nov 20, 2010, at 12:00 PM, fis-requ...@listas.unizar.es wrote:

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than Re: Contents of fis digest...
Today's Topics:

1. footnote to fluctuon discussion (Stanley N Salthe)

*From: *Stanley N Salthe ssal...@binghamton.edu
*Date: *November 20, 2010 9:18:18 AM EST
*To: *...@listas.unizar.es
*Subject: **[Fis] footnote to fluctuon discussion*

Folks -- This cut is Figure 1 from

Sejnowsky, T., 2006.  The computational self. * Annals of the New York

Note that the levels are found to be orders of magnitude different in
size.  No change in any single unit at any level can have an effect at the
next upper level

STAN

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```

### [Fis] footnote to fluctuon discussion

```Folks -- This cut is Figure 1 from

Sejnowsky, T., 2006.  The computational self. * Annals of the New York

Note that the levels are found to be orders of magnitude different in size.
No change in any single unit at any level can have an effect at the next
upper level

STAN
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```

### Re: [Fis] INTELLIGENCE INFORMATION (by Y.X.Zhong)

```Gordana --

interpreted.  In living systems each generation makes a new interpretation
based upon changed conditions of life. But in this case there is not more
(genetic) information, but rather recently altered information -- history
rewritten according to the latest interpretation of recent conditions.  Some
might call this process 'intelligence'. This is the (neo)Darwinian
patterns of information, which is indeed what appears in the fossil record
(as well as in human discourse).  To build more requires preservation and
interpretation. In the physical world, this image is captured in the
asteroid impacts on the moon, with subsequent hits deforming, but not
erasing, the original one.  Information here increases, but not, I think,
intelligence.  Intelligence, I think, lies more in reinterpretation than in
the building more that may follow upon it.

STAN
(Pedro -- this is a new week, so this is my first)

On Sat, Nov 13, 2010 at 5:28 PM, Gordana Dodig-Crnkovic
gordana.dodig-crnko...@mdh.se wrote:

I suppose semioticians are interested in an individual human’s
sense-making in a context of human society.

Or perhaps a social animal’s sense making.

What I think about is how life forms organize to produce increasingly
complex patterns of information processing.

Gordana

*From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
*On Behalf Of *Stanley N Salthe
*Sent:* den 13 november 2010 23:03

*To:* fis@listas.unizar.es
*Subject:* Re: [Fis] INTELLIGENCE  INFORMATION (by Y.X.Zhong)

Concerning:

The minimal claim would be that there is no intelligence without
information. For an agent, intelligence is the ability to face the world in
a meaningful way and it increases with the number of different ways an agent
is able to respond with.

It seems to me that this implies, in any non-mechanistic system, semiosis
-- that is to say, a process of interpretation by the agent.  Thus,
intelligence would be related to the viewpoint of the agent, which would be
located by its needs.  Semioticians, however, have not been much engaged by
this concept.  Hoffmeyer claims that it is especially a social skill.

STAN

On Sat, Nov 13, 2010 at 4:18 PM, Gordana Dodig-Crnkovic
gordana.dodig-crnko...@mdh.se wrote:

Dear Colleagues,

Relating information with intelligence seems to me important for several
reasons. I will try to suggest that intelligence might be a good conceptual
tool if we want to anchor our understanding of information and knowledge in
the natural world.
Yixin mentions the problem of three approaches to AI which exist
independently, based on the methodological doctrine of divide and conquer.
We agree that divide and conquer is just not enough, it is the movement in
one direction, and what is needed is the full cycle -bottom up and top down
- if we are to understand biological systems.

The appropriate model should be generative - it should be able to produce
the observed behaviors, such as done by Agent Based Models (ABM) which
includes individual agents and their interactions, where the resulting
global behavior in its turn affects agents' individual behavior. Unlike
static objects that result from a divide and conquer approach, agents in
ABM are dynamic. They allow for the influence from bottom up and back
circularly. Central for living organisms is the dynamics of the
relationships between the parts and the whole.

Shannon's theory of communication is very successful in modeling
communication between systems, but it is a theory that presupposes that
communication exists and that mechanisms of communication are known. On the
other hand if we want to answer the question why those systems communicate
at all and what made them develop different mechanisms of communication we
have to go to a more fundamental level of description where we find
information processes and structures in biological systems. Natural
computation such as described by Rozenberg and Kari in The many facets of
natural computing
http://www.csd.uwo.ca/~lila/Natural-Computing-Review.pdf includes
information processing in living organisms.

Generative models of intelligence may be based on info-computational
approach to the evolution of living systems. Three basic steps in this
construction are as follows:
. The world on its basic level is potential information.
(I agree with Guy on his information realism)
. Dynamics of the world is computation which in general is information
processing (natural computationalism or pancomputationalism)
. Intelligence is a potential for (meaningful) action in the world. (I
agree with Josph)

The minimal claim would be that there is no intelligence without
information. For an agent, intelligence is the ability to face the world in
a meaningful way and it increases```

### Re: [Fis] Fwd: [Fwd: Discussion Colophon] From J.Brenner

```Replying to Loet.  Well, I may or may not be be a nominalist (which kind?)
in the sense that I believe that qualia are actual as universals, and that
evolution has created entities -- us -- that can experience them, or focus
them, acutely.  This is the same as universals created by language -- such
as 'space', 'heat', etc., all of which do relate to experience but not to
specific objects.

However, I also believe that each species of sentient beings has its own
'take' on actuality, lives in its own 'umwelt', and so my sense of, for lack
of a better term, a 'numinous realm' may be conditioned by my own sense
organs, and further conditioned again by my cultural heritage.  Thus, I am
constructed as: {physico-chemical world {biology {primate {culture {my
experience}, showing the layers of information affording me.

STAN

On Thu, Nov 4, 2010 at 10:32 AM, Loet Leydesdorff l...@leydesdorff.netwrote:

Dear Joe, Stan, and colleagues,

It occurred to me that this is in a certain sense a repeat of the
nominalism/realism discussion. With his heavy emphasis on being/not-being,
Joe is on the realist side, while Stan’s qualia are nominalistic. I assume
that they don’t dwell around like the Greek Gods, but are reflexive
constructs shaped in scholarly discourse that clarifies them. This
discussion makes also clear to me why Joe’s approach is called “Logic in
Reality” and not “Reality in Logic”. Eventually, the grounding has a
direction.

I would consider the vagueness as tangential to the scholarly discourse;
the external referent. The further specification – the updating of
hypotheses – enables us to define new puzzles and thus perhaps to improve
the specification. This reality (as cogitatum part of res cogitans) cannot
be captured with derivatives from “esse”. One would need derivatives from
“frangere” – fractals, fragments, fragile – for the understanding. The
models remain volatile albeit more symbolically generalized than common
language.

With 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 ; http://www.leydesdorff.net/

*From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
*On Behalf Of *Stanley N Salthe
*Sent:* Thursday, November 04, 2010 3:05 PM
*To:* fis@listas.unizar.es
*Subject:* [Fis] Fwd: [Fwd: Discussion Colophon] From J.Brenner

-- Forwarded message --
From: *Stanley N Salthe* ssal...@binghamton.edu
Date: Thu, Nov 4, 2010 at 10:03 AM
Subject: Re: [Fis] [Fwd: Discussion Colophon] From J.Brenner
To: Pedro C. Marijuan pcmarijuan.i...@aragon.es

A comment on Joseph's concluding statement:  It seems clear to me that
there is a world of qualia (spiritual realm, sentience, Peirce's 'universal
mind', whatever).  I believe that the connection between this and the
physical/material world has increased in sharpness/definiteness at certain
locales (like the earth) during the development of the universe.  It does
not, however, seem plausible that this connection is made 'from the bottom
up' via the QM realm, as in Conrad's 'fluctuons'.  The glut of levels in the
material world just presents too many barriers for that to be the case.
Development generally goes from vaguer to increasingly more definite, and
our awareness of qualia likely has had that kind of development,
individually during our ontogeny.

STAN

On Thu, Nov 4, 2010 at 6:24 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

(For unknown reasons this message didn't went through last Tuesday---P.)

Mensaje original

*Asunto: *

The Fluctuon Model; Colophon

*Fecha: *

Tue, 02 Nov 2010 12:44:48 +0100

*De: *

Joseph Brenner joe.bren...@bluewin.ch joe.bren...@bluewin.ch

*Responder a: *

Joseph Brenner joe.bren...@bluewin.ch joe.bren...@bluewin.ch

*Para: *

Pedro C. Marijuan pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es,
fis fis@listas.unizar.es fis@listas.unizar.es

Dear All,

Pedro has asked me to renew with an earlier FIS Group practice and write a
colophon for our discussion of the fluctuon model of Michael Conrad.
Actually, not much has happened with regard to evidence for or against.
There is a lot of information in the latest StanLoet exchange, however,
that has made the exercise worthwhile. There has also been a discussion of
fluctuations, but essentially of fluctuations in *our* thermodynamic
world. Most interesting, but of no direct help with the original task.

I therefore now exercise my editorial authority by offering, by way of
colophon, and with his agreement, the notes of a discussion I had with Pedro
in Beijing. They were not and are not proposed as science, information
science or other; but I like to think they are more than just opinion. For
people, and I assume```

### [Fis] Fwd: [Fwd: Discussion Colophon] From J.Brenner

```-- Forwarded message --
From: Stanley N Salthe ssal...@binghamton.edu
Date: Thu, Nov 4, 2010 at 10:03 AM
Subject: Re: [Fis] [Fwd: Discussion Colophon] From J.Brenner
To: Pedro C. Marijuan pcmarijuan.i...@aragon.es

A comment on Joseph's concluding statement:  It seems clear to me that there
is a world of qualia (spiritual realm, sentience, Peirce's 'universal mind',
whatever).  I believe that the connection between this and the
physical/material world has increased in sharpness/definiteness at certain
locales (like the earth) during the development of the universe.  It does
not, however, seem plausible that this connection is made 'from the bottom
up' via the QM realm, as in Conrad's 'fluctuons'.  The glut of levels in the
material world just presents too many barriers for that to be the case.
Development generally goes from vaguer to increasingly more definite, and
our awareness of qualia likely has had that kind of development,
individually during our ontogeny.

STAN

On Thu, Nov 4, 2010 at 6:24 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es
wrote:

(For unknown reasons this message didn't went through last Tuesday---P.)

Mensaje original   Asunto: The Fluctuon Model; Colophon
Fecha:
Tue, 02 Nov 2010 12:44:48 +0100  De: Joseph Brenner
joe.bren...@bluewin.ch joe.bren...@bluewin.ch  Responder a: Joseph
Brenner joe.bren...@bluewin.ch joe.bren...@bluewin.ch  Para: Pedro C.
Marijuan pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es, fis
fis@listas.unizar.es fis@listas.unizar.es

Dear All,

Pedro has asked me to renew with an earlier FIS Group practice and write a
colophon for our discussion of the fluctuon model of Michael Conrad.
Actually, not much has happened with regard to evidence for or against.
There is a lot of information in the latest StanLoet exchange, however,
that has made the exercise worthwhile. There has also been a discussion of
fluctuations, but essentially of fluctuations in *our* thermodynamic
world. Most interesting, but of no direct help with the original task.

I therefore now exercise my editorial authority by offering, by way of
colophon, and with his agreement, the notes of a discussion I had with Pedro
in Beijing. They were not and are not proposed as science, information
science or other; but I like to think they are more than just opinion. For
people, and I assume that is some of us, who have ever pondered such deep
issues, these notes may suggest some ideas and comments. For others, for
whom talk of Being and Nothingness or Non-Being, *pace* Sartre, is pure
nonsense, pure non-information, I have some sympathy. The only point I would
take issue with is the pure . . .

1. We are aware of our atoms and molecules and those of others through our
adjacencies to them. They have Being for us; they are Being. The
corresponding changes in their states constitute information at several
levels.

2. Our atoms and molecules are composed of strings of which we are *not
* aware. They have no Being for us, they are Non-Being. Whether any
fluctuations or changes in strings can constitute information is not clear.

3. Non-Being has been described both scientifically and traditionally, *
e.g.* the Mind of God, the quantum vacuum, holomovement.

4. Spontaneity and indeterminism (randomness) are possible, but only in
Non-Being. These are reflected in Being only in radioactive decay and
in catastrophic cosmological phenomena (black holes).  The shifts of
perspective in this note are non-random.

5. We in Being are aware of the existence of Non-Being, therefore, as
something internal and external to us at the same time. The LIR Principle of
Dynamic Opposition (PDO) describes this epistemological and ontological
state-of-affairs as real and logical.

6. Non-Being is not and does not have to be aware of itself nor of us here
in Being. We take care of that little function for it.

7. The influence of Non-Being and its changes, *e.g.*, in local
information content. which are not perceived by nor interact with us in the
usual manner, may be due to our awareness of Non-Being, which is a *kind*of
with Non-Being (the unmanifest world) also exist and can influence
biological states. These two perspectives may or may not converge.

8. In either case, the information content of vacuum fluctuations and the
informational content of our awareness/understanding of it and them are, by
the PDO, and at the current state of knowledge, the same and not the same.

9. The existence of a direct energetic (thermodynamic) relationship or
information transfer between Being and Non-Being, as in the fluctuon
model, below the quantum level, remains an open question, but such a
relationship may not be necessary as a basis for information theory.

10. An alternate basis is available in the self-duality and dualities of
energy, at and above the quantum level```

### Re: [Fis] Tactilizing processing

```Bob --

On Fri, Oct 29, 2010 at 3:14 PM, Robert Ulanowicz u...@umces.edu wrote

Subject: Re: [Fis] Tactilizing processing
To: Stanley N Salthe ssal...@binghamton.edu
Cc: u...@cbl.umces.edu

Quoting Stanley N Salthe ssal...@binghamton.edu:

I suggested that a single small scale fluctuation near thermodynamic
equilibrium might have an upscale effect if a larger scale configuration
was
in place (perhaps by way of a larger scale fluctuation) that was able to
be
impacted by that fluctuation in such a way as to alter its configuration
in
a way that would be preserved long enough for it to be detected by a still
larger scale configuration, thus letting one signal go from micro through
meso to macro.  But, for this to be other than a passing event, this would
require some kind of system for which such information might be adaptive,
and so it would be specially organized in such a way as to play this game
rather than being limited to the well-known physical model of ensemble
detection of lower scale events.  Or it would just be a passing accidental
synchronization of fluctuations at different scales.

Stan, Isn't the upward propagation of a small event to the next level
Prigogine's order through fluctuations? (Not across two levels though.)
Bob

The Prigogine model is part of the background of my statement above.
In the Prigogine case, the process of self-organization is pulled by
entropy production intensification as a result of a particular level of
available free energy (more than could be dissipated by conduction, and not
so much as to result in turbulence).  The experimental setup is organized so
as to obtain the resulting dissipative structure.  As well, the energy flows
in this case of 'order through fluctuations' are not individual molecule
fluctuations at the lower level being propagated to the higher level as
seemingly suggested by Conrad's thinking, but a simultaneous reorganization
of the whole system of flow from disorganized to organized.  I don't THINK
that anyone has suggested that this transition is seeded by the fluctuation
of a single molecule in the fluid.  The fluctuations Prigogine had in mind
were, I think, manifest at the scale of the flow itself, which 'searches'
through various configurations to find the one that is stable at the given
flow level in the given set of boundary conditions.  Are you aware of any
suggestion that these variations are seeded by individual fluid molecules
and then amplified upscale?

STAN

- End forwarded message -

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### Re: [Fis] Tactilizing processing

```Jorge -- Then, it is hard to get away from the model where, in 'downward
causation', large scale signals impact simultaneously many small scale
processes, while in upward causation, small scale signals need to accumulate
into some kind of ensemble message.  But Conrad 'fluctuons' seem to be
trying to get beyond this 'standard physical model'.  In a paper :

Salthe, S.N., 2005,b.  Asymmetry and self-organization.  Symmetry, Culture
and Science 16: 71-90.

I suggested that a single small scale fluctuation near thermodynamic
equilibrium might have an upscale effect if a larger scale configuration was
in place (perhaps by way of a larger scale fluctuation) that was able to be
impacted by that fluctuation in such a way as to alter its configuration in
a way that would be preserved long enough for it to be detected by a still
larger scale configuration, thus letting one signal go from micro through
meso to macro.  But, for this to be other than a passing event, this would
require some kind of system for which such information might be adaptive,
and so it would be specially organized in such a way as to play this game
rather than being limited to the well-known physical model of ensemble
detection of lower scale events.  Or it would just be a passing accidental
synchronization of fluctuations at different scales.

STAN

On Fri, Oct 29, 2010 at 8:19 AM, Jorge Navarro López
jnavarro.i...@aragon.es wrote:

Dear Stan  Joseph,

My interpretation of M. Conrad views in that wonderful abstract is that most
molecular recognition events are per se isolated or followed by some very
specific pathway. Then in many cases an accessory tool is needed to
integrate their specific molecular work into the general cellular processes.
In that sense, second messengers are reading and measuring the outcome of
quite many microscopy happenstances and driving to a mesoscopic, highly
amplified value of their own concentrations (e.g., calcium ions, AMP-cyclic,
glycerol... ). This mesoscopic value  is broadcast then through Brownian
motion to a variety of targets, putting into action other microscopic and
mesoscopic processes, etc.
In summary, my view  is that second messengers represent the transition
from many micro- to a meso- and then to many other micro- and so on, in this
way driving the general percolation of information flows (Pedro has also
written about the measurement roles of second messenger within signaling
systems of eukaryotes): I am more interested in the prokaryotes and I am
currently working in the signalome of *M. tuberculosis* (any help will be
welcome!! it is awfully complex).

Best wishes,

Jorge

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### [Fis] Stan to Loet

```Loet --

On Sun, Oct 17, 2010 at 1:43 PM, Loet Leydesdorff l...@leydesdorff.net
wrote:

Dear Stan,

Wasn’t it Tycho Brahe’s suscipio descipiendo, descipio suscipiendo? Nothing
but uncertainty; if order emerges, selection mechanisms must have been
specified.

S: If uncertainty emerges, particular choices must have been specified.

I hesitate: it seems to me that randomness (maximal uncertainty) is the
basic assumption and that order needs to be explained.

I should explain a bit more fully.  By 'uncertainty', I was using
this term to label the situation where definite choices appear to an agent
that must choose a path or action.  So, my view implies an ordered (First
Person) agency. This agency could be as simple as an abiotic dissipative
structure.  So, I see that an ordered agency needs to accompany uncertainty,
and, indeed, helps to locate the situation of any such agent.  If we go to a
more primitive (purely physical, or Peircean 'tychastic') situation, without
any agents, this is where I would say there can be no uncertainty -- unless
a Third Person (another agent) is observing that physical situation. So, if
you can explain order you will have implicitly explained uncertainty as
well. Thus, we could parse the evolutionary situation as {Gaussian physical
locale - {added bounding constraints - {emerged agency}}}, with
uncertainty coming in in the innermost subclass.

STAN

Otherwise, I agree with most of your points. We should not move too easily
from probability functions to (continuous) probability density functions.
The Shannon formulas provide us with a calculus in the discrete domain, that
is, the one where differences prevail.

Best wishes,

Loet

My reply was not based on assuming agency, but on Shannon-type information.
Observed information (by an agent) should be distinguished from expected
information.

It was my point that there could not be expectation unless there was
an observer, even if that observer was of the most general kind.  That is,
both expectation and observer would have to have been the products of
evolution.

Perhaps, you can appreciate this difference in our assumptions in your reply
to the list?

If one assumes that our physical (mathematical) constructs predate the
origin of Western-style science, then your point is well-taken.

STAN

Best wishes,

Loet
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### Re: [Fis] Recapping the discussion? Joseph's Recap

``` mechanisms are not given. Who would have been the One who could have given
them to us other than our various intellects and their interacting
discourses?

Just so!

Fortunately, I don’t send this on a Sunday morning. J

Fear not!  I would suppose that you have been absolved by your own
intellect.

STAN

With best wishes for a nice Saturday,

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 ; http://www.leydesdorff.net/

*From:* fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es]
*On Behalf Of *Stanley N Salthe
*Sent:* Friday, October 15, 2010 3:35 PM
*To:* fis@listas.unizar.es
*Subject:* Re: [Fis] Recapping the discussion? Joseph's Recap

I would like to comment upon Conrad's statement:

When we look at a biological system we are looking at the face of the
underlying physics of the universe... The picture is not one of
simple upscale percolation. The higher levels act down scale on the
lower levels to redefine their fundamental characteristics... the flow

of influence is thus circular as well as vertical, with multiple inner

loops. The circularity is imperfect; complete self-consistency is never
attainable...
This appears in Conrad (1996, BioSystems vol. 38 p. 108).

This message has been advanced in more detail in my own studies,
published in:

1986.  Evolving Hierarchical Systems. Columbia University Press (Conrad;'s
work up to then informed this book)

1993.  Development and Evolution. MIT Press (Chapter 3)

2002.  Summary of the principles of hierarchy theory.  General Systems
Bulletin 31: 13-17. (I am updating this paper, and am willing to send a copy
to anyone who requests it.)

The 'devil is in the details' as they say.  From that point of view,
Conrad's the flow of influence is thus circular as well as vertical, with
multiple inner loops. requires a lot of work, which I have laid some
groundwork for in the above listed texts.

STAN

-
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
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### Re: [Fis] Recapping the discussion? Joseph's Recap

```I would like to comment upon Conrad's statement:

When we look at a biological system we are looking at the face of the
underlying physics of the universe... The picture is not one of
simple upscale percolation. The higher levels act down scale on the
lower levels to redefine their fundamental characteristics... the flow

of influence is thus circular as well as vertical, with multiple inner

loops. The circularity is imperfect; complete self-consistency is never
attainable...
This appears in Conrad (1996, BioSystems vol. 38 p. 108).

This message has been advanced in more detail in my own studies,
published in:

1986.  Evolving Hierarchical Systems. Columbia University Press (Conrad;'s
work up to then informed this book)
1993.  Development and Evolution. MIT Press (Chapter 3)
2002.  Summary of the principles of hierarchy theory.  General Systems
Bulletin 31: 13-17. (I am updating this paper, and am willing to send a copy
to anyone who requests it.)

The 'devil is in the details' as they say.  From that point of view,
Conrad's the flow of influence is thus circular as well as vertical, with
multiple inner loops. requires a lot of work, which I have laid some
groundwork for in the above listed texts.

STAN

-
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
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### Re: [Fis] [Fwd: physics and information]-From Jacob Lee

```Replying to Guy --

You are right.  My favorite examples of signals moving across scales
(e.g.,direct interactions) are (a) lightning, where a signal from the planet
scale system directly contacts an organism at a lower scale, and (b) cancer,
where a single cell can destroy a multicellular organism at a higher scale.
But it can't do this without first growing a population, increasing its
scale.  So, such instances of cross scale signal transitions tend to be
disruptive.  As Simon proposed, the stability of the world depends to some
extent on its being layered into different-scale domains.

What you are asking for -- a physics-neutral theory of information is, I
think not possible in our culture.  Science is our dominant conceptual
institution, and physics is its basis (with logic as ITS foundation).  The
sciences can be displayed thus, in a subsumptive hierarchy: {logic {physics
{chemistry {biology {psychology {sociology}}, with the last two possibly
reversed.  There can be no statement in any science that would be
incompatible with physics.  Having said that, we can see that physics has
been trying to broaden itself via quantum mechanics.  But note the tern
'mechanics' here.  Our culture is predisposed to mechanistic models.  But
every day we experience 'qualia', and these do not seem to be involved with
anything in that hierarchy. Hence we have radical dualisms -- the epistemic
cut, mind / matter, map / territory, OR, internalism / externalism.

STAN

On Wed, Oct 6, 2010 at 4:18 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es
wrote:

Mensaje original   Asunto: physics and information  Fecha:
Tue, 05 Oct 2010 19:23:34 -0700 (PDT)  De: Jacob I Lee
jacob...@csufresno.edu jacob...@csufresno.edu  Para: Pedro C. Marijuan
pcmarijuan.i...@aragon.es pcmarijuan.i...@aragon.es  CC:
fis@listas.unizar.es

Hello,

The recent discussion of the fluctuon model has made me curious about how
closely a theory of information must be wedded to physics. I want to think
of a theory of information that is independent of any particular model of
physics, but this seems perilous when, for example, such things as the
simultaneity of events across frames of reference may have at one time been
taken as axiomatic. At some level of abstraction is there a
physics-neutral theory of information universally applicable to any possible
physics?

My questions are assuredly naive, but naivety is the source of all
questions.

Best,

Jacob
www.jacoblee.net

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### Re: [Fis] replying to Kevin and to Joseph

```Guy -- This is a key idea. 'Mediation' refers to the transformation /
transduction of signals at a boundary (in general it refers to no direct
transfer across boundaries).  In the case before us, that boundary is
between systems that exist / function at different scales.  Note, then, that
a photon impact upon a rhodopsin molecule in a retina is not, AS SUCH,
information to the owner of the retina, but many simultaneous photon impacts
would be transformed into neuron depolarizations, which, in the aggregate,
can activate an awareness of brightness, color, whatever, in the brain. This
creates meaning by / for the larger organization. All of this depends upon
the organization of the system.  In a simpler example, photons can have
unmediated action upon, say, minerals in a rock, with no immediate effect
upon the general shape of the rock at a larger scale, or on its part in a
landscape at a still larger scale.  The photon 'information' did not get
mediated to those levels.

So, yes, information -- transformed at every boundary -- can percolate
across levels, but it is not SAME information, AS information, at the upper
level that it might be at the lower.  Each level creates its own version of
the original signal.  You could say that each level has its own 'language'.
(For examples, organisms can't do what we call 'evolve', species cannot do
what we call 'develop'.)  In the case in point, rhodopsin can change
conformation, but it cannot have increased blood flow (as in the brain).
This is important because it shows the necessity for such transformations to
be constructed in order for evolution to create higher level -- here larger
scale -- entities that are still in contact with the world in general, as
represented in {physicomaterial world {biological world}}.  Biology, and
even molecular biology, exists at a larger scale than fermion - boson
transformations.

As you can see, there is nothing 'new' here, except sensitivity to the
details of system organization. Acknowledging the discontinuities in a
system can only give our models greater verity.

STAN

On Fri, Oct 1, 2010 at 4:46 PM, Guy A Hoelzer hoel...@unr.edu wrote:

Hi Stan,

I don’t understand your notion of “mediated” information flow across levels
of organization.  What do you mean by mediation, and what difference does it
make in the current context?  Isn’t the important thing that information
often does percolate across levels?

Regards,

Guy

On Fri, Oct 1, 2010 at 4:46 PM, Guy A Hoelzer hoel...@unr.edu wrote:

Hi Stan,

I don’t understand your notion of “mediated” information flow across levels
of organization.  What do you mean by mediation, and what difference does it
make in the current context?  Isn’t the important thing that information
often does percolate across levels?

Regards,

Guy

On 10/1/10 1:23 PM, Stanley N. Salthe ssal...@binghamton.edu wrote:

On Tuesday, Sep 28, 2010 at 6:29 PM, Kevin Kirby ki...@nku.edu mailto:
ki...@nku.edu  wrote:

-snip-

On flows across scales, this itself need not be mysterious. Take a single
photon hitting a rhodopsin molecule in the retina of a vertebrate then
[...long chain here...] triggering a fight-or-flight response. Is that a
flow across scales? Sure.

No!  Are you asserting that a brain will respond to a single tickled
rhodopsin molecule? The retina needs to be regaled with more than that in
order to trigger a biological response.  The rhodopsin molecule exists at
the chemical level in nature's hierarchy, and at that level electrons /
photons (IN plural) can have effects because of the chemical organization,
and so, these are not direct, unmediated effects.  Biological synthesis
mediates between these effects and consciousness.  Put otherwise, a single
photon carries no information for biology.  The statement I defend is that
‘no information transits unmediated across scales’. The hierarchy in this
case can be viewed either as [cell [rhodopsin [photonS]]] or as {energy flow
{chemical reaction { biological organization}}}.  Curiously, I am getting
the feeling that hierarchy, after being ignored for decades, is now being
taken as 'ho-hum' -- old hat!

On Wed, Sep 29, 2010 at 11:05 AM, Joseph Brenner
joe.bren...@bluewin.chmailto:
joe.bren...@bluewin.ch  wrote:

Dear Gordana and All,

-snip-

2. This judgment is confirmed :-) by the citations: a) One can agree (I do)
with Floridi's interpretation of reality as the totality of structures
interacting with one another, but we still do not know what a structure is,
ontologically, and there is a caesura with the implication for information;
b) Referring to physicists who say that reality is fundamentally
informational is begging the question at issue.

3. It is not quite accurate to say that Floridi's Levels of Organization
(LoOs) give access to an ontological side that will enable us to see an
informational reality for two reasons: a) we```

### [Fis] replying to Kevin and to Joseph

```Replying to Kevin --

On Tuesday, Sep 28, 2010 at 6:29 PM, Kevin Kirby ki...@nku.edu wrote:

-snip-

On flows across scales, this itself need not be mysterious. Take a single
photon hitting a rhodopsin molecule in the retina of a vertebrate then
[...long chain here...] triggering a fight-or-flight response. Is that a
flow across scales? Sure.

No!  Are you asserting that a brain will respond to a single tickled
rhodopsin molecule? The retina needs to be regaled with more than that in
order to trigger a biological response.  The rhodopsin molecule exists at
the chemical level in nature's hierarchy, and at that level electrons /
photons (IN plural) can have effects because of the chemical organization,
and so, these are not direct, unmediated effects.  Biological synthesis
mediates between these effects and consciousness.  Put otherwise, a single
photon carries no information for biology.  The statement I defend is that
‘no information transits unmediated across scales’. The hierarchy in this
case can be viewed either as [cell [rhodopsin [photonS]]] or as {energy flow
{chemical reaction { biological organization}}}.  Curiously, I am getting
the feeling that hierarchy, after being ignored for decades, is now being
taken as 'ho-hum' -- old hat!

On Wed, Sep 29, 2010 at 11:05 AM, Joseph Brenner joe.bren...@bluewin.ch
wrote:

Dear Gordana and All,

-snip-

2. This judgment is confirmed :-) by the citations: a) One can agree (I do)
with Floridi's interpretation of reality as the totality of structures
interacting with one another, but we still do not know what a structure is,
ontologically, and there is a *caesura *with the implication for
information; b) Referring to physicists who say that reality is
fundamentally informational is begging the question at issue.

3. It is not quite accurate to say that Floridi's Levels of Organization
(LoOs) give access to an ontological side that will enable us to see an
informational reality for two reasons: a) we have not established that
reality is primarily informational nor what this might mean (see above); b)
LoOs, to quote Floridi do support an ontological approach, according to
which systems *for analysis *(my emphasis) are supposed to have a
structure in themselves *de re*, which is allegedly captured and uncovered
by its description. For example, levels of communication, of decision
processing and of information flow can all be presented as specific
instances that can be analyzed in terms of LoOs. However, I submit that we
are still dealing, here, with epistemological constructions.

S: LoOs are hierarchical structures, are in fact compositional
hierarchies (the ones that interdict unmediated information flow across
levels separated by scale).  Hierarchies are conceptual tools, allowing us
to simplify our models of the world -- levels of OBSERVATION are obviously
epistemological tools (he also uses levels of abstraction). No one can
assert that the world itself has this kind of structure (though it does seem
to in many aspects).

-snip-

5. On the question of it 'or' bit, I suggest that bits are the simplest,
most abstract elements of information, constitutive of its lowest semantic
level. Its are something more, for example, as Kevin Kirby said,
fluctuons can perfectly well be looked at as its, given their apparent
interactive characteristics. Understanding the relationship (one or more ?)
between information and matter/energy may be easier if we consider that we
might be talking about the same thing from two perspectives.

S: From a developmental point of view, 'bits', being crisp and
digital, would be end points of material evolution, which could be modeled
thus (using a subsumptive hierarchy): {vagueness - {fuzziness -
{crispness}}}  One could say that only some parts of the world could be
modeled as fuzzy, and even fewer as crisp.
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### Re: [Fis] Revisiting the Fluctuon Model

```Folks --

Comments upon Kirby’s  Brenner’s ‘Opening Remarks’

(1) I used Conrad’s early information-based work in developing my conception
of the scale/compositional hierarchy as applied to material systems.  As a
materialist, I may have ‘mis-read’ his work.  I think this now, upon
glimpsing this ‘fluctuon theory’, which is clearly not a materialist
construct.  Rather, it seems to lie in the realm of mathematical idealism.

Admittedly, materialism may turn out to have been a ‘wrong turn’ in our
attempts to understand the universe.  Information itself may not be a
materialist proposition!  My own thinking is really ‘bit’ from ‘it’!  Then,
fluctuons may really be ‘its’, and not ‘bits’!  Surely ‘bits’ emerged into
the world with information theory, crisp as that is.  I argue that any
development must go from vaguer to more definite, as with any embryo.  Bits
ain’t vague.  Or, tell me HOW they are vague.  Fluctuons as limned here seem
pretty vague to me – perhaps because language cannot reach their
mathematical crispness!

We do not yet have a fuzzy version of cosmology, I suppose.

“Vertical flows” directly “up and down” the scale hierarchy contradicts one
of the principles of that hierarchy in application, which requires
transduction of information in order to cross scales (example: a higher
level constructs statistical representations of lower level dynamics).  That,
of course would be in the ‘manifest, material world’.  And it is precisely
‘information flows’ that would be interdicted at scale changes.

“Percolation networks” to foster a “logical approach” to information flows
across hierarchically organized compartments may seem OK in math.

“Interaction” between manifest organisms and the “unmanifest vacuum” is
tantalizing, but… in information theory?  “Fascinating and rich”, yes.

That these unmanifest communications are “not susceptible to being washed
out by thermal fluctuations”, I suppose follows from the definition of
‘unmanifest’, but organisms seem to be manifest.  What are we reaching for
here?  Transcendence of material limitations as the world goes sour on us?

STAN

Let me add that in my evening musings, I do entertain thoughts that might
well be more crisply informed by fluctuon theory!

On Fri, Sep 24, 2010 at 7:49 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

(The previous message was truncated, sorry. I am sending it again. ---P.)

*THE NATURE OF MICROPHYSICAL INFORMATION:*

*REVISITING THE FLUCTUON MODEL*

*Kevin G. Kirby
*Department of Computer Science
Northern Kentucky University (US)

*Joseph Brenner*
International Center for Transdisciplinary Research
Paris (France)

1. OPENING REMARKS
(Kevin Kirby)

In the standard view, taken for granted so completely it is rarely
articulated, the fundamental physics of particles and fields is a mere
platform for life. Physics and biology are surely deeply different: the
extreme ends of the scales simply don't match up.  For example, the notion
that somehow the incompatibility of general relativity with quantum physics
has some relevance for life seems nonsensical.

But is it? In a series of papers published throughout the 1990s, Michael
Conrad put together a theory in which life was, as he often put it, an image
of the underlying physics of the universe. The mere title of one of the
final papers in the series, and the title of the book he wanted to write,
Quantum Gravity and Life, seems almost like a non sequitur. And indeed,
the theory he put forth was difficult. But the claim I would like to put
forward is that there are deep ideas here that -- even if the full details
of the theory are not correct or not well-defined-- help us reach a more
satisfying theory of information in the natural world.

Tragically, Conrad passed away in 2001, and was unable to complete his
book. Yet a very thorough description remains of his ideas in a series of
sixteen papers from 1989 through 1998.  This work centered on what he
called fluctuon theory. The main exposition was in a series of papers
Fluctuons I,II, III published in Chaos, Solitons and Fractals during
1993-1996.  For the purposes of this discussion, two briefer papers can be
recommended as providing good summaries of his ideas here:

* Conrad, M., 1995, Multiscale synergy in biological information
processing. Optical Memory and Neural Networks 4(2), 89-98.

* Conrad, M., 1998, Quantum gravity and life, BioSystems 46, 29-39.

The fluctuon theory asserts that the universe is a kind of giant homeostat,
but one in which the ground state is always in flight. The universe slides
in and out of consistency.  His starting point was the Dirac sea of
negative energy particles: his vacuum was a plenum.  There was more than
one sea. One was of electrons and positrons, where photons are chains of
such pairs. The gluons of the strong nuclear force were to be chains in a
quark/anti-quark sea. Gravitons were chains that arose from all massive
```

### Re: [Fis] Beijing FIS Group

```On Mon, Sep 20, 2010 at 9:26 AM, Stanley N Salthe ssal...@binghamton.eduwrote:

Regarding the question:  What is your

opinion about Leroy E. Hood' words: Biology Is an
Informational Science?

In a general sense the meaning is that, although every locale in the world
is mediated by history -- requiring information to be understand beyond
knowledge of physical and material laws -- biological systems have
internalized and replicate the results of historical accident as preserved
in the information in the genetic system.  In general, history passes away,
but biological systems capture some of it in the form of species and variety
differences.

STAN

On Mon, Sep 20, 2010 at 8:26 AM, Jorge Navarro López
jnavarro.i...@aragon.es wrote:

Dear Xueshan,

Is the creation of Systems Biology related to Genomics,
Proteomics, Transcriptomics, Glycomics, and many many other
-mics? If so, what is the relationship between the Systems
Biology and information from the x-mics angle?

It is a very good question. In my practical experience, the omic
disciplines provide a lot of data, usually compiled into data-bases, so that
one can obtain many lists of parts about most processes and cellular
subsystems. But in many cases that info is insufficient. For instance I am
working in the signaling system of *Mycobacterium tuberculosis* and, if I
go to the tuberculist data base, I can obtain more than two hundred
transcriptional factors presumably related to signaling functions (belonging
either to the one, two or three-component systems), however the true
signaling function of each component is very difficult to obtain (a painful
task one-by-one, searching at the literature). Thus I have to spent a lot of
time to get a systemic  or general approach, and even more if I want to
build some models...
Systems Biology is like ecology, that has to deal with the integration of
a lot of partial  specialized information from many other disciplines.

What is your
opinion about Leroy E. Hood' words: Biology Is an
Informational Science.

I think (it is a very personal opinion!, obviously influenced by Pedro)
that the leaders of Bioinformatic and Systems Biology (Gilbert, Hood,
Brenner, Kitano, etc.) are not very serious in that type of statements. What
they mean is that biology and molecular biology are becoming not really
information sciences but intensive computer science users. Usually one
doesn´t find very deep theoretical reflexion in these guys although their
works are very good from the technical point of view.

Are there any difference between transmitter in Neuroscience
and hormone in Endocrinology from the viewpoint of
information transmission and communication ?

Neurobiology is not my turf. Raquel will answer you  very soon about
that.

By the way, do you know anyone working on Systems Biology in your
University?

Nice to talk to you!

Jorge

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### Re: [Fis] Curious chronicle

```Pedro -- This sentiment seems odd to me.  This is because I have retired to
an out-of-the-way rural area and no longer travel to conferences, and so my
only contact with other than family members is through e-mail, including
lists. And my wife does all our communications with the locals.  I do NOT
feel lonely, etc. at all. It seems like the perfect setup to me!  Every day
I find new messages from all over the world.  In what way is my situation
different from all those lonely persons?  Could it be my 'cold' Scandinavian
genome?  Or simply my age?

STAN

On Thu, Jul 22, 2010 at 11:10 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Dear Wolfgang, Rafael, Joseph... and FIS Collegues,

Very briefly, as I am incurring in a forbidden three per week, I see the
general problem with ICT  social networks as an information glut. It is
very similar to the parallel epidemics of obesity in affluent contemporary
societies. In the same way that our bodies are not very well equipped for
the sedentary life style and the overconsumption of food --and this is
clearly written in the genes selected during our long history as
hunter-gatherers-- we are also ill-equipped to deal with the diminishing
structure of meaningful social bonds around us and the increase of junk
information.  Parallel to obesity, there is a current, silent epidemics of
loneliness, depression, psychogenic pain, suicide... How to counter that?
Very difficult problem, but knowing better what is the sociotype, or say
the ranges of social structures akin to our genetic inheritance, would help
to identify better cultural alternatives and lifestyles, including better
uses for ICT presumably.

A careful discussion should involve social networks (network science),
social brain hypothesis, evolutionary paleoanthropology, neuroscience, ICT,
cultural analysis, etc., and above all and a nice information science
integration. We are far from knowing *Homo informationalis!

*best *

Pedro

*
Wolfgang Hofkirchner escribió:

dear pedro,

what you mention here is just what bothers me since long. in the scientific
literature about the internet (both empirical and kind of philosophical)
there are two positions to be found:

the first position is the optimistic one in which the potentialities of the
new media are praised and the technical support for establishing new ties
(bonds with people) are appreciated. the second position is rather
cultural-critical and bemoans the rubbish that is multiplied by the net and

i, for my part, guess, the truth is a little bit more complicated. the new
ties you can establish are not only strong ties that you strengthen by
technology (e.g. when i was abroad i skyped with my family) but also and
predominantly weak ties that promote a kind of irresponsibility because you
can enter a community and – that's more important – leave it whenever you
want without sanctions being there. thus my research question: how can we
shape icts in order to foster real communities?

wolfgang

http://hofkirchner.uti.at/

Am 21.07.2010 um 12:10 schrieb Pedro C. Marijuan:

Dear Rafael, Bob, and FIS Colleagues

Thanks a lot for the erudite comment and the elegant Latin. I quite
agree about that challenging aspect. However, I keep thinking that the
whole new communication technologies are adding to the decreasing
sociotype of individuals in todays' society. Like TV in the previous
generation, they provide an easy amusement but at the cost of a tighter
budget in the daily time needed for socialization. Like other
Anthropoids (following the Social Brain Hypothesis) we need around 20
% of time devoted to social grooming, to languaging, laughing etc. in
a variety of social groups. Do not paying on a daily basis this
evolutionary debt conduces to disappointment, frustration, depression,
unhappiness... My point is that the whole ITC are bringing extra
opportunities for a variety of e-contacts but at the same time are
diminishing the social grooming. This could be searched out throughout
the notion of sociotype summarizing the connective structure around
the individual, and  would need specific inter-multi-cultural
researches, and above all achieving more concretion around a series of
indicators.

much appreciated. In next exchanges I would like to introduce some
further ideas. Maybe human social networks as gauged by the sociotype
could also benefit of the ascendancy approach (metrics abouts
parenthood, relatives, friendships, acquaintances, etc.) Who knows.

very list about the subject (1997-98?), or was it in some FIS Proceedings?

all the best

Pedro

Rafael Capurro escribió:

Dear Pedro and all,

in an article selected by the Sueddeutsche Zeitung of The New York
Times of today (July 19) with the title The Mediuim matters ```

### Re: [Fis] Curious chronicle

```Has anyone suggested the function of contact sports to be the 'moral
equivalent' of war.  Many young men requires this kind of excitement because
of their hormone mix.

STAN

On Mon, Jul 19, 2010 at 10:55 AM, Pedro C. Marijuan
pcmarijuan.i...@aragon.es wrote:

Dear FISers,

Looking for an informational explanation of soccer, or other sports, as was
asking Joseph, one can look at the internal side of the event. Then, as
Jorge and Bob have done, one can discuss about the panorama of networking
relationships or the ascendancy of the different elements. While agreeing
with the interest of these approaches, one can also look towards the outside
and ask about the social importance attributed to such type of spectacles.
It is interesting that today a lot of economic activities, like sports, may
be ascribed  to ephemeral information production --think of entertainment,
news, fashions, e-networks, communications, tourism, etc. Maybe this is the
fastest growing segment, even in spite of the global crisis. Why the
increasing predominance of panem et circenses?
An speculative point may be that complex societies are caught into a
information paradox. The higher they grow in their aggregate complexity the
lower the structure of basic social relations (and interesting information)
around the individual. According to Dunbar's social brain hypothesis,
these complex societies deviate progressively from the evolutionary
networking structure of our species. Thus info surrogates of whatever type
are more and more necessary for the individual and for the society as a
whole, although probably they are working worse and worse. If this is so, it
makes sense that in the information era depression has become the first
incapacitating pathology (above flu).

Unfortunately, the victory at the world championship has been so ephemeral!

best wishes

Pedro
PS. As a question to Karl: in what extent are directed graphs (or generic
networks) equivalent to multidimensional partitions? Would it make sense the
description of ascendancy in terms of partitions?

Robert Ulanowicz escribió:

Dear Jorge and Fis members:

The method is intriguing, but rather ad-hoc.

I and colleagues in marine science have directly used
information-theoretic indexes to evaluate the dynamically most
important nodes and links in a quantified network. I'm convinced it
could be applied as well to players on a team:

Ulanowicz, R.E. and D. Baird. 1999. Nutrient controls on ecosystem
dynamics:  The Chesapeake mesohaline community.  J.  Mar.
Sys. 19:159-172

The best,
Bob Ulanowicz

-
Robert E. Ulanowicz|  Tel: +1-352-378-7355
Arthur R. Marshall Laboratory  |  FAX: +1-352-392-3704
Department of Biology  |  Emeritus, Chesapeake Biol. Lab
Bartram Hall 110   |  University of Maryland
University of Florida  |  Email u...@cbl.umces.edu
u...@cbl.umces.edu
Gainesville, FL 32611-8525 USA |  Web http://www.cbl.umces.edu/~ulan
http://www.cbl.umces.edu/~ulan
--

Quoting Jorge Navarro López jnavarro.i...@aragon.es
jnavarro.i...@aragon.es:

Dear FIS collegaes,

Hi!  This is my first posting in the list. My name is Jorge Navarro
and I am working with Pedro on Systems Biology and Network Science.
Following with Joseph proposal I have found an interesting paper
about a satisfactory theory of information  applicable to  teamwork
sports:

*Quantifying the Performance of Individual Players in a Team Activity*
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010937

I think that formally one can say  a lot about what teamship
activities become interesting and exciting to watch, and what other
activities are dull and boring.
I was playing soccer myself until a few years ago (forward), like
Villa :-), and I am very interested in the informational side of
sports, soccer of course.

VIVA ESPAÑA!!!

Kind Regards

Jorge

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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
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