Dear Pedro, Terry, Bob L., Bob U., Loet, Gordana and All,
I have been in transit from Switzerland to California and only now have a 
moment to even start to comment on what has become for me one of the most 
interesting and useful exchanges on the list. 
I would like to try to summarize my position as follows: I agree with Terry's 
mechanism and I disagree with his model. As others have said much better than 
I, Terry has made a major contribution to information science (and philosophy) 
with his description of orthodynamic, morphodynamic and teleodynamic processes. 
It can and should form the basis of all claims that informational processes can 
have reference and display significance. 
On the other hand, for reasons that I cannot completely express, the autogenic 
model system does not, as they say here in the U.S. "work" for me. It is stated 
to be simple, the simplest model, and the possibility exists that it is too 
simple. We are by now all in agreement about the shortcomings of autopoesis. 
But in a similar vein, in my paper in Information on Terry's book, Incomplete 
Nature, I suggested that the discussion of 'information as absence', a profound 
concept introduced by Terry, needed to be supplemented by maintenance, in part, 
of 'information as presence'. Reciprocal autocatalysis, also, is by no means a 
concept that does not still retain many assumptions, for example, how is 
reciprocity achieved, what are its implications and what is the meaning of 
'auto'. Essential aspects of the evolutionary dynamics of information may be 
inexpressible in the current autogenic model due to what appear to me to be a 
lack of sufficiently deep roots in quantum mechanics.
I thus see a very valuable ontological (pace Jeremy) critique of Terry's work 
in progress from at least five or six perspectives, including my own.
Thank you and best wishes for 2015,
----Message d'origine----
De :
Date : 18/01/2015 - 13:22 (PST)
À :
Cc :
Digest, Vol 10, Issue 11
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 
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 
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,
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:
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, 
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 
 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 
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 
 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 
 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.
2015-01-17 9:00 GMT-02:00 <>:
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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'" <>
Date: Fri, 16 Jan 2015 12:43:40 +0100
Subject: Re: [Fis] Beginnings and ends---Steps to a theory of reference & 
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!
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 
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)
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
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