Hi Pedro,

Jeremy Sherman here, a long-time pirate. Pleased to meet you. You say:

I am also critical with the autogenesis model systems--wouldn't it be far
clearer approaching a (relatively) simple prokaryotic cell and discuss upon
its intertwining of the communication and self-production arrangements? The
way a bacterium "sees" the world, and reorganizes its living, could be a
very useful analysis. I think it leads to a slightly different outcome
regarding reference/significance, and meaning/value/fitness.

Terry and the Pirates have a long standing rule: One cannot employ as
explanation that which hasn't yet been explained. Failing to hold this
standard opens researchers up to merely taxonomical work, positing forces,
properties and capacities defined solely by their consequences, in effect
mistaking questions as answers. Hence, our focus on exploring reference at
its earliest possible emergence, and explaining exactly how that emergence
occurs, since emergence is also a question, not an answer, an explanandum
not an explanan.

Somewhat related, I recently came across this:

*Epistemological particularism* is the belief that one can know something
without knowing how one knows that thing.[1]
<http://en.wikipedia.org/wiki/Epistemological_particularism#cite_note-1> By
this understanding, one's knowledge is justified before one knows how such
belief could be justified. Taking this as a philosophical approach, one
would ask the question "What do we know?" before asking "How do we know?"
The term appears in Roderick Chisholm
<http://en.wikipedia.org/wiki/Roderick_Chisholm>'s "The Problem of the
Criterion <http://en.wikipedia.org/wiki/Problem_of_the_Criterion>", and in
the work of his student, Ernest Sosa
<http://en.wikipedia.org/wiki/Ernest_Sosa> ("The Raft and the Pyramid:
Coherence versus Foundations in the Theory of Knowledge"). Particularism is
contrasted with Methodism
<http://en.wikipedia.org/wiki/Methodism_(philosophy)>, which answers the
latter question before the former. Since the question "What do we know"
implies that we know, particularism is considered fundamentally
anti-skeptical, and was ridiculed by Kant
<http://en.wikipedia.org/wiki/Immanuel_Kant> in the*Prolegomena

We Pirates do what we can to stay on the epistemological methodist side of

Even the simplest prokaryotic cell is extraordinarily complex. We don't
want to run before we can walk.  The briskest runners-before-walkers are
those who want to go straight from physics to human consciousness, a leap
that we think makes the endeavor thoroughly intractable.



On Thu, Jan 8, 2015 at 4:48 AM, Pedro C. Marijuan <pcmarijuan.i...@aragon.es
> wrote:

> Dear Terry and colleagues,
> Thanks a lot for the opening text! It is a well crafted Essay full of very
> detailed contents. My impression is that the "microphysics" of information
> has been solved elegantly --at least at the level of today's relevant
> knowledge-- with your work and the works of related authors, one of them
> Karl Friston, who could be linked as a complementary approach to yours (in
> particular his recent "Life as we know it", Royal Society Interface
> Journal, 10: 20130475). His Bayesian approach to life's organization,
> coupled with (variational) "free energy" minimization principle, conduces
> to the emergence of homeostasis and a simple form of autopoiesis, as well
> as the organization of perception/action later on. Thus, quite close to
> your approach on autogenic systems. About the different sections of the
> Essay, the very detailed points you deal with in section 4 ("steps to a
> formalization of reference")  are, in my opinion, the  conceptual core and
> deserve a careful inspection, far more than these rushed comments. In any
> case, the relationship Boltzmann-Shannon entropies has been cleared quite
> elegantly.
> However, for my taste the following sections have not sufficiently opened
> the panorama. And with this I start some critical appreciations. Perhaps
> the microphysics of information is not the critical stumbling block to me
> removed for the advancement of the informational perspective. We could
> remain McLuhan's stance on Shannon's information theory and von Neumann's
> game theory... yes, undoubtedly important advancements, but not the
> essential stuff of information. But in this list there are people far more
> versed in McLuhan's contents and whether the caveats he raised would
> continue to apply (obviously in a different way). I am also critical with
> the autogenesis model systems--wouldn't it be far clearer approaching a
> (relatively) simple prokaryotic cell and discuss upon its intertwining of
> the communication and self-production arrangements? The way a bacterium
> "sees" the world, and reorganizes its living, could be a very useful
> analysis. I think it leads to a slightly different outcome regarding
> reference/significance, and meaning/value/fitness.
> If we look at the whole view of the "information world" (human societies,
> behaving individuals, brain organization, cellular processes, biomolecules)
> and how a myriad of information flows are crisscrossing, ascending,
> descending, focusing, mixing and controlling energy flows, etc. we may have
> an inkling that this evanescent world paradoxically becomes the master of
> the physical world (the "fluff" versus the "stuff", Lanham 2006), and that
> is organized far beyond the rules of the micro-macro-physical world. But
> how? What are the essentials of this magnificent "castle in the air"
> (reminding Escher's engrave: http://fis.sciforum.net/ )?
> In next exchanges I will try to ad some more specifics on the above
> "fluffy" comments, derided from a fast reading of the Essay. Thanks again,
> Terry, for providing us this discussion opportunity in the New Year.
> best  ---Pedro
>> _*Steps to a theory of reference & significance in information
>> *_*FIS discussion paper by Terrence W. Deacon (2015)*
>> This is the link to download the whole paper: https://www.dropbox.com/s/
>> v5o8pwx3ggmmmnb/FIS%20Deacon%20on%20information%20v2.pdf?dl=0
>> /"The mere fact that the same mathematical expression - Σ pi log pi
>> occurs both in statistical
>> mechanics and in information theory does not in itself establish any
>> connection between these
>> fields. This can be done only by finding new viewpoints from which
>> thermodynamic entropy and
>> information-theory entropy appear as the same concept." /(Jaynes 1957, p.
>> 621)
>> /"What I have tried to do is to turn information theory upside down to
>> make what the
>> engineers call 'redundancy' [coding syntax ] but I call 'pattern' into
>> the primary
>> phenomenon. . . . “/ (Gregory Bateson, letter to John Lilly on his
>> dolphin research, 10/05/1968)
>> *Introduction*
>> In common use and in its etymology the term ‘information’ has always been
>> associated with
>> concepts of reference and significance—that is to say it is about
>> something for some use. But
>> following the landmark paper by Claude Shannon in 1948 (and later
>> developments by Wiener,
>> Kolmogorov, and others) the technical use of the term became almost
>> entirely restricted to refer
>> to signal properties of a communication medium irrespective of reference
>> or use. In the
>> introduction to this seminal report, Shannon points out that although
>> communications often have
>> meaning, “These semantic aspects of communication are irrelevant to the
>> engineering problem”
>> which is to provide a precise engineering tool to assess the
>> computational and physical demands
>> of the transmission, storage, and encryption of communications in all
>> forms.
>> The theory provided a way to precisely measure these properties as well
>> as to determine
>> limits on compression, encryption, and error correction. By a sort of
>> metonymic shorthand this
>> quantity (measured in bits) came to be considered synonymous with the
>> meaning of
>> ‘information’ (both in the technical literature and in colloquial use in
>> the IT world) but at the cost
>> of inconsistency with its most distinctive defining attributes.
>> This definition was, however, consistent with a tacit metaphysical
>> principle assumed in the
>> contemporary natural sciences: the assertion that only material and
>> energetic properties can be
>> assigned causal power and that appeals to teleological explanations are
>> illegitimate. This
>> methodological framework recognizes that teleological explanations merely
>> assign a locus of
>> cause but fail to provide any mechanism, and so they effectively mark a
>> point where explanation
>> ceases. But this stance does not also entail a denial of the reality of
>> teleological forms of
>> causality nor does it require that they can be entirely reduced to
>> intrinsic material and energetic
>> properties.
>> Reference and significance are both implicitly teleological concepts in
>> the sense that they
>> require an interpretive context (i.e. a point of view) and are not
>> intrinsic to any specific physical
>> substrate (e.g. in the way that mass and charge are). By abstracting the
>> technical definition of
>> information away from these extrinsic properties Shannon provided a
>> concept of information that
>> could be used to measure a formal property that is inherent in all
>> physical phenomena: their
>> organization. Because of its minimalism, this conception of information
>> became a precise and
>> widely applicable analytic tool that has fueled advances in many fields,
>> from fundamental
>> physics to genetics to computation. But this strength has also has
>> undermined its usefulness in
>> fields distinguished by the need to explain the non-intrinsic properties
>> associated with
>> information. This has limited its value for organismal biology where
>> function is fundamental, for
>> the cognitive sciences where representation is a central issue, and for
>> the social sciences where
>> normative assessment seem unavoidable. So this technical redefinition of
>> information has been
>> both a virtue and a limitation.
>> The central goal of this essay is to demonstrate that the previously set
>> aside (and presumed
>> nonphysical) properties of reference and significance (i.e. normativity)
>> can be re-incorporated
>> into a rigorous formal analysis of information that is suitable for use
>> in both the physical (e.g.
>> quantum theory, cosmology, computation theory) and semiotic sciences
>> (e.g. biology, cognitive
>> science, economics). This analysis will build on Shannon’s formalization
>> of information, but will
>> extend it to explicitly model its link to the statistical and
>> thermodynamic properties of its
>> physical context and to the physical work of interpreting it. It is
>> argued that an accurate analysis
>> of the non-intrinsic attributes that distinguish information from mere
>> physical differences is not
>> only feasible, but necessary to account for its distinctive form of
>> causal efficacy.
>> Initial qualitative and conceptual steps toward this augmentation of
>> information theory have
>> been outlined in a number of recent works (Deacon 2007, 2008, 2010, 2012;
>> Deacon &
>> Koutroufinis, 2012; Deacon , Bacigaluppi & Srivastava, 2014). In these
>> studies we hypothesize
>> that both a determination of reference and a measure of significance or
>> functional value can be
>> formulated in terms of how the extrinsic physical modification of an
>> information bearing
>> medium affects the dynamics of an interpreting system that exhibits
>> intrinsically end-directed
>> and self-preserving properties.
>> [...]
>> A model system
>> To test these principles and their relationship to reference and
>> significance, I and my
>> colleagues have conceived of an empirically realizable and testable
>> thought experiment. As in
>> most efforts to formalize basic physical properties it is useful to begin
>> with a simple model
>> system in which all aspects of the process can be unambiguously
>> represented. For our purposes
>> we describe a theoretical molecular system called an autogen, which
>> maintains itself against
>> degradation by reconstituting damaged components and reconstituting
>> system integrity. This
>> model system involves an empirically realizable molecular complex
>> described previously
>> (Deacon 2012; also in Deacon & Cashman 2012; and also called an autocell
>> in Deacon 2006a,
>> 2007; 2009; and Deacon & Sherman 2008).
>> [...]
>> In this way we can use formal and simulated versions of autogenesis to
>> develop a measure of
>> relative significance, in the form of “work saved.” I hypothesize that
>> this simple model system
>> exemplifies the most basic dynamical system upon which a formal analysis
>> of informational
>> interpretation and significance can be based.
>> [...]
>> In both forms, modifications of the autogenic process is provided with
>> information referring
>> to its own preservation via boundary conditions (external or internal)
>> that are predictive of
>> successful self-preservation. The significance of information of either
>> sort is assessed by the
>> relative minimization of work per work cycle, and therefore the decreased
>> uncertainty of selfreferential
>> constraint preservation. In this way interpretation is analogous to the
>> decrease in
>> uncertainty that is a measure of received information in Shannonian
>> theory, but at a teleodynamic
>> system level.
>> Using these three variants of a simple model system I claim that we can
>> precisely analyze the
>> relationships between information medium properties, intrinsically
>> end-directed work, and the
>> way these enable system-extrinsic physical conditions to become
>> referential information
>> significant to system ends. These relationships are not only simple
>> enough to formalize, but they
>> can be simulated by computer algorithms at various levels of logical and
>> physical detail. I
>> believe that creating and experimenting with these simulated autogenic
>> systems will enable us to
>> reframe the mysteries of reference and significance as tractable
>> problems, susceptible to exact
>> formal and empirical analysis. This is still a far cry from a theory of
>> information that is
>> sufficiently developed to provide a basis for a scientific semiotic
>> theory much less than an
>> explanation of how human brains interpret information, but it may offer a
>> rigorous physical
>> foundation upon which these more complex theories can be developed.
>> *— Terry*
>> Professor Terrence W. Deacon
>> University of California, Berkeley
>>  -------------------------------------------------
> Pedro C. Marijuán
> Grupo de Bioinformación / Bioinformation Group
> Instituto Aragonés de Ciencias de la Salud
> Centro de Investigación Biomédica de Aragón (CIBA)
> Avda. San Juan Bosco, 13, planta X
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.i...@aragon.es
> http://sites.google.com/site/pedrocmarijuan/
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