References for Deacon comments (Jan 18)

Deacon, T. W. (2012) Incomplete Nature: How Mind Emerged from Matter.
W. W. Norton & Co., New York .

Haldane, J. B. S. (1954) The origin of life. New Biol 16, 12–27.

Kant, I. (1790/1952) The Critique of Judgement: II Teleological
Judgement. Trans. J. C. Meredith. The Great Books, No. 42, 550–613.
University of Chicago Press, Chicago.

Kauffman, S. (2000) Investigations. Oxford University Press, New York.

Maturana, H. and F. Varela, F. (1980) Autopoiesis and Cognition: The
Realization of the Living. Boston Studies in the Philosophy of Science
43, D. Reidel, Dordrecht.

On 1/18/15, Terrence W. DEACON <> wrote:
> 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 <>
> wrote:
>> 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 <
>>> 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.
>>>  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
>>> 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.
>>>   From: Jeremy Sherman <>
>>> Date: Sunday 18 January 2015 03:41
>>> To: fis <>
>>> 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 <
>>>> 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 <>:
>>>>> Send Fis mailing list submissions to
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>>>>> or, via email, send a message with subject or body 'help' to
>>>>> You can reach the person managing the list at
>>>>> When replying, please edit your Subject line so it is more specific
>>>>> 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" <>
>>>>> To: "'fis'" <>
>>>>> 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.es
>>>>> -------------------------------------------------
>>>>> _______________________________________________
>>>>> Fis mailing list
>>>>  --
>>>>   Moisés André Nisenbaum
>>>> Doutorando IBICT/UFRJ. Professor. Msc.
>>>> Instituto Federal do Rio de Janeiro - IFRJ
>>>> Campus Maracanã
>>>> _______________________________________________
>>>> Fis mailing list
>> --
>> Professor Terrence W. Deacon
>> University of California, Berkeley
> --
> Professor Terrence W. Deacon
> University of California, Berkeley

Professor Terrence W. Deacon
University of California, Berkeley

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