Hi Joseph,

Indeed there is much more to discuss than I could include in this
already too long discussion paper. The related "absence" issues are of
course critical to my thinking. I value your continued feedback on
these issues as well.

I think you do a quite adequate job of restating the autogenesis
hypothesis in your first paragraph. I also agree with your comment
about the model of autogenesis being incomplete because it does not
specify the necessary stereochemical properties of the interacting
molecules, or for that matter the energy flux that is required to
drive reciprocal catalysis, the shapes and charges of molecules that
tend to self assemble into containers (like viral capsids), the
rate-coupling required for reciprocal catalysis and self-assembly to
be reciprocally supportive, and the entropy production of the whole
process, etc., etc. Yes, much simulation and lab work lies ahead.

I actually don't see a problem there, however, nor do I think this
results in circularity. Nothing at the molecular level smuggles in
properties that define information in the model. All that matters for
my purpose is that I am not postulating any unrealistic atomic and
molecular properties.

When Ludwig Boltzmann used an idealized thought experiment for
formulate his atomistic account of the 2nd law of thermodynamics with
particles that didn't even interact, it was sufficient to model the
general logic of entropy increase. No real atoms, no real physics,
just the logic of time and random change in position. The model
captured what was minimally necessary and no more. Yes, Gibbs and
others fine-tuned the account, adding the role of free-energy and many
dimensions of interactions, but Boltzmann's thought experiment laid
the foundation. So I don't consider the abstraction involved in the
autogenesis model to be an intrinsic fatal flaw. The question is
whether or not it is too simple, or whether it violates some basic
physico-chemical principles. I can't see how you can doubt that it is
a realistic model, since both component processes are well-studied
molecular phenomena with innumerable exemplars available. Only the
linkage between them that constitutes autogenesis lacks a know
empirical exemplar. It is an empirical question whether this can
occur, and what conditions and types of molecules this would require.
I see no physico-chemical reason to doubt this possibility.

Your question about "qualitative signification" and my concept of
"work saving" seemed to lead inexplicably into a comment about "human
and social history." Lost me there. But you also seemed to suggest
that the autogenic model provided no fixed ground for making a
qualitative assessment (significance). I believe that it does.

In the autogentic model this depends on there being a fixed amount of
chemical work required to reconstitute an autogenic complex from a
specific state of disaggregation. This differential can be assigned a
finite repeatable value (again not specifying specific molecules).
This functionally defined threshold provides the reference value that
I argue is required for assessing the "significance" of information.
It is both a qualitative state difference (non-algorithmic in your
terms) and yet the product of a quantitative work differential.

This "assessment" is best exemplified by the second autogenic model
system; i.e. with the shell that loses integrity with increasing
numbers of bound catalytic substrates. The threshold value of its
transition from intact-inert to disaggregated-and-dynamically
reconstituting provides an assay of the environmental potential for
re-achieving stability and preserving this same potential to be
available for another work cycle. Different threshold values will
result in different amounts of work required for reconstitution and
different probabilities of persistence with respect to disruption. The
threshold that determines this change of state is thereby representing
a property of the environment that is of qualitative value with
respect to the perpetuation of this system's assessment capacity into
the future, irrespective of any outside interpretation. And since
differences in thresholds will provide better or worse fits between
work required and resources provided, there can be predictive value
differences of the information provided by this change of state.
Differences in its conveyance of information "predictive"  of the
nearby (though not just directly contiguous) environment's supportive
or non-supportive value.

OK. It's clearly too simple for modeling human knowledge, subjective
awareness, the "meaning" of this sentence, etc., but I think it's a
useful first step beyond Shannon.

— Terry

On 1/30/15, joe.bren...@bluewin.ch <joe.bren...@bluewin.ch> wrote:
> Terry,
> In your discussion paper, you state that an interpretive process can only be
> adequately defined with respect to a process that is organized to maintain
> itself by repairing and reconstituting its essential form and dispositions -
> a teleodynamic process. I agree with this definition. Your model, further,
> is that of a theoretical two-component molecular system called an autogen
> that is capable of instantiating such, autogenic processes. The properties
> of the model molecules are stated to be those of real molecules – reciprocal
> autocatalysis and self-assembly and these processes are further stated to be
> self-organizing. The model, it is claimed, can analyze the relationships
> between the information medium properties, the work involved and the
> properties of the context, the environment or as you put it the
> system-extrinsic physical conditions.
> What I see as having been elided here is that in the real systems, but not
> in the model as described, one has the properties of the molecules that
> enable them to ‘self’-assemble in the first place. Unless these are taken
> into account, I claim that the models are incomplete. They require inclusion
> of the residual constraints (potentialities) at lower levels of molecular
> structure to avoid the danger of circularity. Further, there seems to be no
> place in this description of relationships for the non-algorithmic
> processes, for example qualitative signification (vs. the ‘amount’ of work
> saved), that are necessarily involved as soon as one leaves the level of
> abstraction of the model. These are well described on p. 10 as “the complex
> system of relationships” involving both human and social history. Wu Kun
> adds their potential states and calls the whole entity the informosome. This
> was the basis for the comment in my first note that I agreed with the
> mechanism but not the model(s).
> My comment about presence being a source of information as well as absence
> refers to your more complete treatment of information as an absential
> phenomenon in Incomplete Nature rather than to that in your discussion
> paper. In the latter, the concepts on p. 3 (inexistent properties) and on p.
> 10 (information as being about an absent referent) should therefore be
> discussed in another thread.  I therefore look forward very much to a further
> round of discussion of real systems using the tools you have provided.
> In this, however, I think there will be agreement between our approaches to
> the necessary dualism of information, despite the differences in language.
> My line is to search for the overlap/dynamic interaction between the two
> sides of the relationship and the chains of intermediating processes (Wu
> again) involved.
> Best wishes,
> Joseph        
>>----Message d'origine----
>>De : dea...@berkeley.edu
>>Date : 30/01/2015 - 12:43 (PST)
>>À : joe.bren...@bluewin.ch
>>Cc : fis@listas.unizar.es
>>Objet : Re: [Fis] Fwd: Re: Concluding the Lecture?
>>Thanks to Joseph for this spirited rejoinder, and to Krassimir for
>>reminding us that convergence is perhaps more likely to succeed than
>>any single-minded approach.
>>With Krassimir, I am in agreement. I have probably overstated the
>>priority of my own approach, even if I do believe it to be a best
>>middle ground from which to begin formalization. This is a big
>>challenge and I should celebrate the diversity of approaches more than
>>I have. This is my path, and I have taken this opportunity to make my
>>reasons for pursuing it clear. Like most of us, it is sent as a sort
>>of mating call, in case others might find interesting insights there
>>In response to Joseph, I would challenge you to specifically identify
>>my homuncular assumptions, demonstrate where the autogenic model makes
>>them, and deacribe in what ways you think that autogenesis is somehow
>>not physically realizable. I admit to being blind to any of these, but
>>I don't want to just convince you, I want to get it right. However, I
>>am not willing to live with unresolved dualisms. And I don't quite get
>>your comment about "dualisms that do exist in nature" and how you
>>connect this with my presence/absence perspective. Perhaps this has to
>>do with the fact that I am not satisfied that certain dualisms arising
>>from quantum theories are fundamental, rather than the result of
>>incomplete theory, and your own view which seems to embrace them. In
>>which case we may need to agree to disagree.
>>I am slightly perplexed and don't quite follow your implications
>>regarding the specific proposal made in this piece. The dualisms I am
>>hoping to resolve in this essay orbit around the difference between
>>physicalistic and semiotic uses of the information concept, and about
>>how this implicitly reifies Descartes' res cogitans / res extensa
>>dualism, with reference and significance on the former side of this
>>divide and Shannon information (and related uses in physics) on the
>>latter. You can read my view as arguing that this dualism cannot
>>merely be left as an unanalyzed assumption if we are seeking a
>>complete theory of information.
>>I anticipate that there is much unmentioned detail that remains to be
>>unpacked and debated here. Pursuing some of these details could be
>>very informative, even if it doesn't change entrenched positions.
>>I think that it is interesting that so many responses have betrayed a
>>sort of thinly veiled irritation and anger. To me it suggest that we
>>are close to a nerve—i.e. some critical issues that are of central
>>Thanks, Terry
>>On 1/30/15, joe.bren...@bluewin.ch <joe.bren...@bluewin.ch> wrote:
>>> Dear Pedro, Dear FISers,
>>>     Terrence Deacon has made a passionate plea for the proper consideration
>>> of
>>> his approach to information science that his contribution merits. But
>>> this
>>> consideration is only possible if he is willing to accept that some of
>>> his
>>> positions may be contaminated with assumptions in a way that he correctly
>>> criticizes in others. As a specific example, we can all easily understand
>>> and agree that the incorporation of ‘homunculi’, that is, unproven
>>> mechanisms, as explanatory, should be avoided. In my view, however, Terry
>>> has a small army of homunculi at work (sic!) who insure that his
>>> processes
>>> of self-organization, self-reconstitution and ‘spontaneous’ self-assembly
>>> can take place! The finality of using his simulated autogenic systems is
>>> “a
>>> rigorous physical foundation upon which” future complex theories of
>>> information may be based. If, as I contend, Terry’s approach has failed
>>> to
>>> take into account the fundamentally dualistic physical properties of real
>>> systems, it is hard to see how it could do so.
>>> In his reply to Loet, regarding cognitive processes, Terry writes: “As I
>>> have said a number of times, my goal is not to deal with all aspects of
>>> the
>>> information concept, and certainly not at the level of human thought. I
>>> merely propose to dissolve the implicit dualism in our current concepts
>>> at
>>> the most basic level, so that for example it will be possible to develop
>>> a
>>> scientifically grounded theory of molecular biosemiotics.” No-one can
>>> argue
>>> with his first sentence, but the second has the implication that dualism
>>> at
>>> the most basic level in concepts should be absent when it is present in
>>> reality. Again, we can all reject the straw-man of mind-body dualism. But
>>> the dualisms that do exist in nature must be reflected in concepts or the
>>> latter are outside nature and outside science. The pair presence-absence
>>> is
>>> one of these that I have offered, so far without comment, as one of
>>> these.
>>> As a substitute for what is referred to as ‘the implicit dualism in our
>>> current concepts’, Terry seems to offer a repeated reliance on the
>>> Peircean
>>> categories as having explanatory power. I have discussed, accessibly, why
>>> these categories amount to epistemic classifications, a position that is
>>> in
>>> fact confirmed by a member of Terry’s group. Ontological approaches,
>>> which
>>> if looked at closely differ from the ones Terry correctly criticizes, are
>>> given a back of the hand dismissal that suggests that the writers may not
>>> be
>>> familiar enough with them to make the distinction.
>>> A point of agreement between Terry and me is that a concept of quantum
>>> information should not be mixed with one of thermodynamic information.
>>> This
>>> does not mean, however, that the some of the dual aspects of quantum
>>> entities are not relevant for thermodynamic processes, including the
>>> properties, production and transfer of information. Terry is absolutely
>>> correct to question the so-called ‘it-from-bit’ theory of information in
>>> its
>>> simplest form. Again, however, alternatives are available at the heart of
>>> which is exactly the ‘overlap’ between physics and information that Pedro
>>> calls for, e.g., those of Luhn and myself.
>>> I think Krassimir has a good point in concluding that we have a problem
>>> of
>>> civilization and that all our efforts, scientific and philosophical,
>>> should
>>> be made with the common good at the center of our preoccupations. This is
>>> the theme of the Vienna Summit 2015. Information offers the ground on
>>> which
>>> standard physical and biological as well as social and psychological
>>> reality
>>> can meet. It is from the most complex, interactive, recursive aspects of
>>> these realities as well as from the simplest that we must learn. Thank
>>> you.
>>> Best wishes,
>>> Joseph
>>>>----Message d'origine----
>>>>De : dea...@berkeley.edu
>>>>Date : 30/01/2015 - 09:31 (PST)
>>>>À : lo...@physics.utoronto.ca
>>>>Cc : fis@listas.unizar.es
>>>>Objet : Re: [Fis] Concluding the Lecture?
>>>>Thanks to Pedro and Bob for these last few comments. Indeed, like
>>>>Darwin in 1859 we are still just beginning to formulate "one long
>>>>argument" that will need to be progressively refined in the decades to
>>>>come. The question is where best to begin the task of synthesizing. I
>>>>too find the metaphor of searching for lost keys quite apropos, but I
>>>>would beg your indulgence while I add an elaboration to this metaphor
>>>>that sheds light on the perspective I have offered.
>>>>Yes, we must at first search close to the light, even though there we
>>>>will only find vague hints. But, importantly, as we cover more and
>>>>more territory we will discover that the light progressively
>>>>brightens. So long as we keep searching and don't walk out into the
>>>>dark too quickly, skipping over important territory in between, the
>>>>entire territory will become more and more thoroughly illuminated,
>>>>searchable, and familiar to us.
>>>>I believe that the light is brightest in the domain where we can see a
>>>>clear relation between the two quite different concepts of entropy and
>>>>the relationship of both to the concept of work. Admittedly, starting
>>>>so minimally as I have in this essay seems remote from the interests
>>>>of psychologists, anthropologists, economists and their kin, who
>>>>demand an account of human-scale information processes, while at the
>>>>same time appearing to introduce the messiness of semiotic concerns
>>>>into the seemingly pristine world of information as a simple physical
>>>>parameter. But of course the problem is to find the best illuminated
>>>>middle ground between these two extremes, both still bathed in the
>>>>darkness of simplifying assumptions that make them seem mutually
>>>>exclusive— separated by darkness.
>>>>This is what I am trying to accomplish. Though deceptively simple, I
>>>>believe that the autogenic model system is just sufficiently complex
>>>>to provide complete illumination of each of the critical defining
>>>>features of the information concept—sign medium properties (entropies,
>>>>uncertainty, constraint), reference (aboutness), significance
>>>>(function, value, normativity), and interpretation (adaptation,
>>>>intelligence)—while not artificially simplifying the issue by ignoring
>>>>one or the other of these facets.
>>>>Because of its simplicity none of these basic concepts are left in the
>>>>dark as black boxes or excluded as taboo concepts. But of course,
>>>>working at such a basic level means that the nature of more complex
>>>>phenomena as thinking, subjectivity, language, and culture (to mention
>>>>only a few) are not yet well illuminated by this light. This isn't to
>>>>suggest that other pursuits in these other domains should be
>>>>abandoned—for they at least clear away some of the underbrush creating
>>>>paths that will help to ease the linkage between the different
>>>>subterritories when finally the light brightens (to continue the
>>>>metaphor). I just believe that this middle level is where the light
>>>>best illuminates all the critical foundational issues.
>>>>I don't expect agreement, but so far I haven't felt that the specific
>>>>components of this proposal have been addressed in this thread. And in
>>>>these closing days of discussion (as well as in future privately
>>>>shared emails after this window closes) I hope to receive some
>>>>suggestions and constructive criticisms pointing to where I might go
>>>>next with this approach.
>>>>Thanks for all your inputs.  Terry
>>>>On 1/30/15, Bob Logan <lo...@physics.utoronto.ca> wrote:
>>>>> Thanks Pedro for your remarks. We have not reached our destination as
>>>>> you
>>>>> point out but the important thing is to enjoy the journey which I
>>>>> certainly
>>>>> have. It is inevitable that with such a slippery concept as information
>>>>> that
>>>>> there will be different destinations depending on the travellers but
>>>>> what
>>>>> I
>>>>> like about FIS in general and the dialogue that Terry prompted in
>>>>> particular
>>>>> is the interesting ideas and good company I encountered along the way.
>>>>> As
>>>>> for your remark about searching where there is light I suggest that we
>>>>> pack
>>>>> a flashlight for the next journey to be led by our tour guide Zhao
>>>>> Chuan.
>>>>> One common theme for understanding the importance of both information
>>>>> and
>>>>> intelligence for me is interpretation and context (figure/ground or
>>>>> pragmatics). Thanks to all especially Terry for a very pleasant
>>>>> journey.
>>>>> -
>>>>> Bob
>>>>> ______________________
>>>>> Robert K. Logan
>>>>> Prof. Emeritus - Physics - U. of Toronto
>>>>> Chief Scientist - sLab at OCAD
>>>>> http://utoronto.academia.edu/RobertKLogan
>>>>> www.physics.utoronto.ca/Members/logan
>>>>> www.researchgate.net/profile/Robert_Logan5/publications
>>>>> On 2015-01-30, at 8:25 AM, Pedro C. Marijuan wrote:
>>>>>> Dear Terry and colleagues,
>>>>>> At your convenience, during the first week of February or so we may
>>>>>> put
>>>>>> an
>>>>>> end to the ongoing New Year Lecture --discussants willing to enter
>>>>>> their
>>>>>> late comments should hurry up. Your own final or concluding comment
>>>>>> will
>>>>>> be appreciated.
>>>>>> Personally, my late comment will deal with the last exchange between
>>>>>> Bob
>>>>>> and Terry, It is about the point which follows:  "...there was no
>>>>>> thesis
>>>>>> other than the word information is a descriptor for so many different
>>>>>> situations and that it is a part of a semantic web - no roadmap only a
>>>>>> jaunt through the countryside of associations - a leisurely preamble."
>>>>>> In my own parlance, we have been focusing this fis session on the
>>>>>> microphysical foundations of information (thermodynamic in this case)
>>>>>> which together with the quantum would look as the definite foundations
>>>>>> of
>>>>>> the whole field, or even of the whole "great domain of information."
>>>>>> But
>>>>>> could it be so? Is there such thing as a "unitary" foundation? My
>>>>>> impression is that we are instinctively working "where the light is",
>>>>>> reminding the trite story of the physicists who has lost the car keys
>>>>>> and
>>>>>> is looking closest to the street lamp.  The point I suggest is that
>>>>>> the
>>>>>> different informational realms are emergent in the strongest sense:
>>>>>> almost
>>>>>> no trace of the underlying information realms would surface. Each
>>>>>> realm
>>>>>> has to invent throughout its own engines of invention the different
>>>>>> informational & organizational  principles that sustain its existence.
>>>>>> It
>>>>>> is no obligate that there will be a successful outcome.... In the
>>>>>> extent
>>>>>> to which this plurality of foundations is true, solving the
>>>>>> microphysical
>>>>>> part would be of little help to adumbrating the neuronal/psychological
>>>>>> or
>>>>>> the social information arena.
>>>>>> The roadmap Bob suggests is an obligatory exploration to advance; we
>>>>>> may
>>>>>> disagree in the ways and means, but not in the overall goal. It is a
>>>>>> mind
>>>>>> boggling exercise as we have to confront quite different languages and
>>>>>> styles of thinking. For instance, the next session we will have at FIS
>>>>>> (in
>>>>>> a few weeks) is an attempt of an excursion on "Intelligence Science".
>>>>>> Presented by Zhao Chuan, the aim is of confronting the phenomenon of
>>>>>> intelligence from a global perspective amalgamating science
>>>>>> (artificial
>>>>>> intelligence), emotions, and art (poetic and pictorial). Not easy, but
>>>>>> we
>>>>>> will try
>>>>>> Anyhow,  Terry, we much appreciate your insights and the responses you
>>>>>> have produced along the Lecture. It was a nice intellectual exercise.
>>>>>> Best wishes to all---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 X
>>>>>> 50009 Zaragoza, Spain
>>>>>> Tfno. +34 976 71 3526 (& 6818)
>>>>>> pcmarijuan.i...@aragon.es
>>>>>> http://sites.google.com/site/pedrocmarijuan/
>>>>>> -------------------------------------------------
>>>>>> _______________________________________________
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>>>>Professor Terrence W. Deacon
>>>>University of California, Berkeley
>>>>Fis mailing list
>>> _______________________________________________
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>>Professor Terrence W. Deacon
>>University of California, Berkeley
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