Typo in line 7 (correction)

experimentally determine whether or *not* it "works" as proposed.

On Sun, Jan 18, 2015 at 1:20 PM, Terrence W. DEACON <dea...@berkeley.edu>

> Gordana's response provides a wonderful opening for digging into some of
> the most challenging and subtle issues lurking behind this essay.
> For now I will respond to the comparison between autopoiesis and
> autogenesis and what can and cannot be learned from each. In many ways this
> comparison is at the center of the conceptual challenge I offer.
> First, autopoiesis is a philosophical concept. Though various model
> systems have been proposed that purport to embody its logic, it is not an
> empirically testable hypothesis that would allow one to experimentally
> determine whether or n to it "works" as proposed.
> Here is the definition that Maturana and Varela provided in 1980:
> [an autopoietic system as one that] "constitutes itself ... as a concrete
> unity ... by specifying the topological domain of its realization ..." "So
> an “autopoietic machine” is one that collectively produces its material
> components as well as the network of relations between them that
> constitutes their unity in a discrete physical location."
> These latter properties are not attributed to any separate and distinctive
> mechanism over and above the closed co-production of components and yet are
> essential defining attributes. Indeed, this organization is described as
> the "fundamental variable which it maintains constant"  (p. 79).
> In simple terms, autopoiesis is a highly abstract account  of what must be
> the case for something to be a living organism. In this respect I consider
> it to be an updated restatement of Kant's concept of the self-organization
> that constitutes an organism, with the added stipulation that it also
> somehow [how?] determines systemic unity and coherence.
> Here is Kant in 1790:
> “An organized being is then not a mere machine, for that has merely motive
> power, but it possesses in itself formative power of a self-propagating
> kind which it communicates to its materials though they have it not of
> themselves.” (p. 558) and “... every part ... is there for the sake of the
> other (reciprocally as end, and at the same time, means).” (p. 557)
> Kant concludes that this isn't sufficient to determine intrinsic teleology
> (and by implication insufficient to determine that the concepts of function
> and adaptation, much less information). And that these are not intrinsic
> attributes of organisms. I believe that that he is right to concludes that
> these attributes alone only provide justification for assuming that
> teleological attribute are descriptive glosses, not intrinsic to
> organisms—assigned from a sort of extrinsic transcendental perspective.
> In a striking parallel, the evolutionary biologist J. B. S. Haldane gave
> the following definition of life in 1929: “A simple organism must consist
> of parts A, B, C, D, and so on, each of which can multiply only in the
> presence of all, or almost all, of the others.” (p. 245)
> The fundamental problem is that the autopoiesis description requires—but
> does not provide—an explanation for how organizational unity is generated
> and maintained. Like Kant and Haldan M & V merely assume the presence of
> some means of maintaining this co-productive unity of interdependent
> components. And yet, it is individuation of a self (a beneficiary) that
> "acts on its own behalf" (to quote Stu Kauffman's definition of autonomous
> agency) that is the critical  feature that enables us to locate intrinsic
> teleological organization.
> I argue that autogenesis is, in contrast, is an empirically testable model
> system, whose attributes can be verified or falsified. That among these
> attributes are those that constitute autonomous agency, self-repair,
> reproduction, and even evolvability in a limited sense. And finally, that
> this is what allows us to precisely identify the intrinsic presence of an
> interpretive dynamic for which reference and significance (i.e. the
> assignment of value) to a discrete physical individuated system. Not
> surprisingly, M & V argue that autopoiesis is a separate phenomenon from
> reproductive, evolutionary, and representational processes (and they deny
> the reality of representation, which is a central attribute being explained
> in my proposal).
> Where we are in agreement, however, is that the dynamic that constitutes
> living should also be the dynamic that constitutes mentality. But given the
> differences listed above and described in my essay, to confuse these two
> concepts is to miss the very essence of my argument. Moreover, as I
> indicated at the conclusion of my essay, the analysis of reference and
> significance that can be formalized using this approach still is a long
> ways from an account of the phenomenology of human subjective experience.
> In Incomplete Nature I argue that mental experience is at least a second
> order variant of the dynamics that characterizes autogenesis.
> So although some have claimed that autogenesis provides an empirically
> realizable exemplar of a process that could be characterized as
> autopoietic, I think that this misses the crucial point. Autopoiesis theory
> fails to even describe what is most essential: the nature of the dynamic
> that generates the coherent individuation of an autonomous agent. Not
> surprisingly, it has nothing constructive to say about information theory
> and how it might be possible to formalize a theory of reference and
> significance. Indeed, as M & V claim, these don't really exist as physical
> phenomena but are rather givens in some sort of solipsistic embodied
> idealism.
> As for studying the problem at many levels from bacterial communication to
> social organization, it should be clear that I believe that the conceptual
> challenge demands that we work at many levels of information science (in
> the broad sense) at once, recognizing that the ultimate goal is to get
> beyond our current methodological dualism. As I noted, my goal in this
> essay is only to work at the very bottom of the problem in recognition of
> the fact that without this most basic foundation the larger goals will
> remain out of reach.
> It is the possibility of legitimizing reference and significance as
> scientific concepts with solid empirical foundation that makes it
> reasonable to imagine such a larger vision, as Pedro has intimated. I
> believe that succeeding at this lowest level project could provide a new
> perspective for understanding subjective and social phenomena, and possibly
> even help to identify and implement a novel approach to "computing."
> — Terry
> On Sun, Jan 18, 2015 at 12:34 AM, Gordana Dodig-Crnkovic <
> gordana.dodig-crnko...@mdh.se> wrote:
>>   Dear colleagues,
>>  Even though I agree with all Jeremy writes in his new post, I would
>> still return back to the opposite side (where Pedro’s previous post left
>> us) and try to think about the big picture.
>> I am sure there will be many FISers who will take the challenge of
>> discussing the details of construction of an autogen as a bridge between
>> meaning and mechanism.
>>  In his first post, Jeremy wrote:
>>  “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 explanans.”
>>  “We Pirates do what we can to stay on the epistemological methodist
>> side of things.”
>> Epistemological methodism is explained as the opposite of epistemological
>> particularism, which is the belief that one can know something without
>> knowing how one knows that thing. So according to epistemological
>> Methodists, for me to know implies not only that I know *that* I know
>> but even that I know *how* I know. It is a very strong assumption.
>>  It seems to me to exclude constructive approaches to knowledge
>> generation. When we construct, we simply use elements that suit the purpose
>> of construction. There is no very hard requirement to understand bricks.
>> How do we conceptualize knowledge and knowing? What does it mean “to know”
>> and “to know that we know”? How detailed, precise and formal knowledge
>> should be for me to claim “I know”?
>> For example I can say: we know that the universe consists of
>> matter/energy in space/time. But how much indeed do we know about it? Only
>> a small fraction (<5%?) of the content of the universe seems to be made of
>> matter/energy while the majority of the universe is made of dark
>> matter/dark energy and at the moment we do not know what they are. This
>> sounds like a very pessimistic view of our present knowledge. However I
>> strongly believe that this state must be temporary and that a new
>> break-through will come soon. It may happen in the similar way as in the
>> time of Planck, who solved the problem of the ultraviolet catastrophe, (a
>> prediction of late 19th century/early 20th century classical physics that
>> an ideal black body at thermal equilibrium will emit radiation with
>> infinite power). Some assumptions (something that we believe we know and we
>> probably even believe that we know why we know) are simply wrong.
>> Knowledge is a dynamic, nonlinear, adaptive, learning system.
>> That is why the suggestion to study information not only on the level of
>> physics and chemistry in a well-defined simplified system, but on many
>> different levels of abstraction is relevant. Some people (Alexej Kurakin
>> for example, (Kurakin, 2011)) see fractal structures that govern generation
>> of information, from atoms to human societies, and one can learn about the
>> properties of one level from the observed patterns on some other levels. The
>> reason to look at the fuzzy “big picture” at the same time as we construct
>> much more coherent, crispy and convincing detailed aspects of it is that
>> they are inseparably connected. The role of unexplained pieces in the
>> theoretical framework is as placeholders. Like in *lazy evaluation*, we
>> do not do anything about it until we learn more at some point.
>>  (In programming language theory, lazy evaluation, or call-by-need[1] is
>> an evaluation strategy which delays the evaluation of an expression until
>> its value is needed (non-strict evaluation) and which also avoids repeated
>> evaluations (sharing).[2][3] The sharing can reduce the running time of
>> certain functions by an exponential factor over other non-strict evaluation
>> strategies, such as call-by-name.
>> http://en.wikipedia.org/wiki/Lazy_evaluation)
>>  This is not meant as a critique of Terry’s approach, which is
>> fascinating elegant, and refreshing among many fuzzy discussions about the
>> nature of reference and significance. However, connections and integration
>> with other levels and perspectives on information might be instructive and
>> worthwhile, especially from Terry who has done so much research on higher
>> levels. Such as e.g. in Harrington et al. (2001). “Science, culture,
>> meaning, values: a dialogue” Annals of the New York Academy of Sciences. and
>> of course even more in Deacon T. (2012) the Incomplete Nature: How Mind
>> Emerged from Matter. Norton & Company
>>  What might be interesting on the synthetic side (as the opposite side
>> of the analytic one as presented in the New Year’s Essay) would be
>> integration of levels that Terry has in the Incomplete Nature, based on the
>> dynamics of information, where information has different meaning on
>> different levels of abstraction/organisation. In the similar way as an
>> autogen, as a self-organizing unit that preserves itself *dynamically*
>> and grows via a combination of autocatalysis and self-assembly, our
>> knowledge grows dynamically and the meaning of pieces changes accordingly.
>> In other words, it is not only self-organizing but also self-generating.
>> Different scientific domains support and regulate each other; different
>> “domain-specific” (or “science-specific”) models can help better
>> construction or generation of knowledge of the whole as well as of the
>> details. Specifically, it might be useful to connect to computing (as
>> information dynamics), as Pedro suggests.
>>  Computing (Rosenbloom, “The Fourth Great Scientific Domain”) seen as
>> information dynamics, goes together with the physical, the biological, and
>> the social. The project of naturalization proceeds by connecting all four
>> domains. (Dodig-Crnkovic, 2014) The attractiveness of the project as
>> Terry’s (as presented in the Incomplete Nature) is in its contribution to
>> the naturalization of reference and significance – concepts that still are
>> highly mystified in the eyes of many.
>>  At the end, I have two questions.
>>  First the particular one. I would like to know what exactly is the
>> difference between autogenesis and autopoiesis? It seems to me that
>> autogenesis as it looks like from Terry’s Opening Essay is a step before
>> the whole system can be integrated and said to be alive. On the other hand 
>> *autopoiesis
>> is the process of life of an organism* such as cell with all properties
>> of a living organism. Autogen seems to me as a chemical automaton while
>> autopoetic system is alive. The theory of autopoiesis is descriptive and
>> qualitative. It does not make the insights made by Maturana and Varela less
>> important. Understanding *autopoiesis as cognition* makes a vital
>> connection between mind and matter. Like Pedro, I also believe that study
>> of the behavior of prokaryotic cells such as bacteria is useful as it can
>> reveal a lot about information processing as social cognition (Ben-Jacob,
>> Becker, & Shapira, 2004; Ben-Jacob, Shapira, & Tauber, 2006, 2011;
>> Ben-Jacob, 2008, 2009a, 2009b) (Ng & Bassler, 2009; Waters & Bassler,
>> 2005).
>>  There is a lot we don't know about such complex systems as bacteria but
>> we can learn relevant things even if we apply “lazy evaluation” strategy
>> for many parts in the model. In other words, it should be possible and
>> reasonable to build knowledge even though we do not know (enough) about
>> parts we build from and their mutual interactions.
>>  My second question, the general one, goes back to Pedro’s post:  how
>> the New Year’s Essay connects to the big picture with four great scientific
>> domains?
>>   With best regards,
>>  Gordana
>>  References
>> Ben-Jacob, E. (2008). Social behavior of bacteria: from physics to
>> complex organization. The European Physical Journal B, 65(3), 315–322.
>> Ben-Jacob, E. (2009a). Bacterial Complexity: More Is Different on All
>> Levels. In S. Nakanishi, R. Kageyama, & D. Watanabe (Eds.), Systems
>> Biology- The Challenge of Complexity (pp. 25–35). Tokyo Berlin Heidelberg
>> New York: Springer.
>> Ben-Jacob, E. (2009b). Learning from Bacteria about Natural Information
>> Processing. Annals of the New York Academy of Sciences, 1178, 78–90.
>> Ben-Jacob, E., Becker, I., & Shapira, Y. (2004). Bacteria Linguistic
>> Communication and Social Intelligence. Trends in Microbiology, 12(8),
>> 366–372.
>> Ben-Jacob, E., Shapira, Y., & Tauber, A. I. (2006). Seeking the
>> Foundations of Cognition in Bacteria. Physica A, 359, 495–524.
>> Ben-Jacob, E., Shapira, Y., & Tauber, A. I. (2011). Smart Bacteria. In L.
>> Margulis, C. A. Asikainen, & W. E. Krumbein (Eds.), Chimera and
>> Consciousness. Evolution of the Sensory Self. Cambridge Boston: MIT Press.
>> Dodig-Crnkovic, G. (2014). Modeling Life as Cognitive Info-Computation.
>> In A. Beckmann, E. Csuhaj-Varjú, & K. Meer (Eds.), Computability in Europe
>> 2014. LNCS (pp. 153–162). Berlin Heidelberg: Springer.
>> Kurakin, A. (2011). The self-organizing fractal theory as a universal
>> discovery method: the phenomenon of life. Theoretical Biology and Medical
>> Modelling, 8(4). Retrieved from http://www.tbiomed.com/content/8/1/4
>> Ng, W.-L., & Bassler, B. L. (2009). Bacterial quorum-sensing network
>> architectures. Annual Review of Genetics, 43, 197–222.
>> Waters, C. M., & Bassler, B. L. (2005). Quorum Sensing: Cell-to-Cell
>> Communication in Bacteria. Annual Review of Cell and Developmental Biology,
>> 21, 319–346.
>>  http://www.ait.gu.se/kontaktaoss/personal/gordana-dodig-crnkovic
>> http://www.mrtc.mdh.se/~gdc/
>>   From: Jeremy Sherman <mindreadersdiction...@gmail.com>
>> Date: Sunday 18 January 2015 03:41
>> To: fis <fis@listas.unizar.es>
>> Subject: Re: [Fis] Fis Digest, Vol 10, Issue 11
>>   It would be satisfying perhaps to think of our collective work as at
>> the forefront of the development of what will become A Grand Domain of
>> Science, but I would say the better trend in current science is toward
>> careful integration between domains rather than toward established grand
>> divisions, which seems a more a classical approach. Doesn't information
>> play out in the biological and the social domains? Isn't our most ambitious
>> goal here to explain scientifically the relationship between information
>> and the physical domain?
>>  Whether modest or foolhardy as Terry suggests or of some other stature,
>> Terry's approach addresses the source of the great schism in all academic
>> and intellectual circles: Physical scientists are appropriately barred from
>> explaining behavior in terms of the value of information for some
>> end-directed self about, or representative of anything. But biological and
>> social scientists can't help but explain behavior in those terms. Focusing,
>> precisely on possible transitions from the physical domain to the living
>> and social domains is exactly what a scientific approach demands.
>>  Lacking an explanation for the transition from mechanism to
>> end-directed behavior (which is inescapably teleological down to its roots
>> in function or adaptation--behaviors of value to a self about its
>> environment), science is stuck, siloed into isolated domains without a
>> rationale.
>>  To my mind, this makes the implications of meticulous work at the very
>> border between mechanism and end-directed behavior anything but modest in
>> its possible implications. In this I agree with Pedro. With what we now
>> know about self-organization-- how it is footing on the physical side for a
>> bridge from mechanism to end-directed behavior but does not itself provide
>> the bridge,  we are perfectly poised to build the bridge itself, through an
>> integrated science that explains the ontology of epistemology, providing
>> solid scientific ground over the absolutely huge gaping hole in the middle
>> of the broadest reaches of scientific and philosophical  endeavor.
>>  Whether Terry's work or someone else's work bridges that gap, I predict
>> that, at long last, the gap can and will be finally filled, probably within
>> the next decade. As ambitious researchers this would be a lousy time for
>> any of us, Terry included, to stick to our guns in the face of substantial
>> critique revealing how a theory we embrace merely provides a new, more
>> clever way way to hide or smear over the gap pretending it isn't there,
>> which is why I would love to see this discussion refocus on the article's
>> detailed content. Though the implications of this research at the
>> borderline may be grand, the research, in the doing, is as Terry implies as
>> modest any careful scientific work.
>>  Jeremy Sherman
>> On Sat, Jan 17, 2015 at 5:06 AM, Moisés André Nisenbaum <
>> moises.nisenb...@ifrj.edu.br> wrote:
>>> Hi, Pedro.
>>> I didnt receive th image (Figure 1. The Four Great Domains of Science)
>>> Would you please send it again?
>>>  Thank you.
>>>  Moises
>>> 2015-01-17 9:00 GMT-02:00 <fis-requ...@listas.unizar.es>:
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>>>> than "Re: Contents of Fis digest..."
>>>> Today's Topics:
>>>>    1. Re: Beginnings and ends---Steps to a theory of reference &
>>>>       significance (Pedro C. Marijuan)
>>>> ---------- Mensagem encaminhada ----------
>>>> From: "Pedro C. Marijuan" <pcmarijuan.i...@aragon.es>
>>>> To: "'fis'" <fis@listas.unizar.es>
>>>> Cc:
>>>> Date: Fri, 16 Jan 2015 12:43:40 +0100
>>>> Subject: Re: [Fis] Beginnings and ends---Steps to a theory of reference
>>>> & significance
>>>>  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 of contemporary disciplines in the background;
>>>> while the superimposed “four-leaf clover” represents the four great
>>>> scientific domains.
>>>> --
>>>> -------------------------------------------------
>>>> 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.iacs@aragon.eshttp://sites.google.com/site/pedrocmarijuan/
>>>> -------------------------------------------------
>>>> _______________________________________________
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>>>  --
>>>   Moisés André Nisenbaum
>>> Doutorando IBICT/UFRJ. Professor. Msc.
>>> Instituto Federal do Rio de Janeiro - IFRJ
>>> Campus Maracanã
>>> moises.nisenb...@ifrj.edu.br
>>> _______________________________________________
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> --
> Professor Terrence W. Deacon
> University of California, Berkeley

Professor Terrence W. Deacon
University of California, Berkeley
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