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

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>:
>>> Send Fis mailing list submissions to
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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/
>>> -------------------------------------------------
>>> _______________________________________________
>>> Fis mailing list
>>> Fis@listas.unizar.es
>>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>  --
>>   Moisés André Nisenbaum
>> Doutorando IBICT/UFRJ. Professor. Msc.
>> Instituto Federal do Rio de Janeiro - IFRJ
>> Campus Maracanã
>> moises.nisenb...@ifrj.edu.br
>> _______________________________________________
>> Fis mailing list
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