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<div><font face="Calibri,sans-serif">Dear colleagues,</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">In his first post, Jeremy wrote:</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">“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.”</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">“We Pirates do what we can to stay on the epistemological methodist side of things.”</font></div>
<div><font face="Calibri,sans-serif">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 <i>that</i> I know but even that I know
<i>how</i> I know. It is a very strong assumption.</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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”?</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif">Knowledge is a dynamic, nonlinear, adaptive, learning system.</font></div>
<div><font face="Calibri,sans-serif">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. </font><span style="font-family: Calibri, sans-serif;">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 <i>lazy evaluation</i>, we do not do anything about it until we learn more at some point. </span></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">(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)</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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. </font><span style="font-family: Calibri, sans-serif;">and of course even more in Deacon T. (2012) the Incomplete Nature: How Mind Emerged from Matter. Norton & Company</span></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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
<i>dynamically</i> 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.</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">At the end, I have two questions. </font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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 <i>autopoiesis is the process of life of an organism</i> 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
<i>autopoiesis as cognition</i> 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). </font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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. </font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div><font face="Calibri,sans-serif">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?</font></div>
<div><font face="Calibri,sans-serif"><br>
</font></div>
<div>
<div>
<div style="font-family: Calibri, sans-serif; font-size: 14px;">With best regards,</div>
</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;">Gordana</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><font face="Calibri,sans-serif">References</font></div>
<div><font face="Calibri,sans-serif">Ben-Jacob, E. (2008). Social behavior of bacteria: from physics to complex organization. The European Physical Journal B, 65(3), 315–322.</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif">Ben-Jacob, E. (2009b). Learning from Bacteria about Natural Information Processing. Annals of the New York Academy of Sciences, 1178, 78–90.</font></div>
<div><font face="Calibri,sans-serif">Ben-Jacob, E., Becker, I., & Shapira, Y. (2004). Bacteria Linguistic Communication and Social Intelligence. Trends in Microbiology, 12(8), 366–372.</font></div>
<div><font face="Calibri,sans-serif">Ben-Jacob, E., Shapira, Y., & Tauber, A. I. (2006). Seeking the Foundations of Cognition in Bacteria. Physica A, 359, 495–524.</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
<div><font face="Calibri,sans-serif">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</font></div>
<div><font face="Calibri,sans-serif">Ng, W.-L., & Bassler, B. L. (2009). Bacterial quorum-sensing network architectures. Annual Review of Genetics, 43, 197–222.</font></div>
<div><font face="Calibri,sans-serif">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.</font></div>
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<div><font size="2"><a href="http://www.ait.gu.se/kontaktaoss/personal/gordana-dodig-crnkovic">http://www.ait.gu.se/kontaktaoss/personal/gordana-dodig-crnkovic</a></font></div>
<div><font size="2"><a href="http://www.mrtc.mdh.se/~gdc" style="color: purple;">http://www.mrtc.mdh.se/~gdc</a>/</font></div>
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<span style="font-weight:bold">From: </span>Jeremy Sherman <<a href="mailto:mindreadersdictionary@gmail.com">mindreadersdictionary@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Sunday 18 January 2015 03:41<br>
<span style="font-weight:bold">To: </span>fis <<a href="mailto:fis@listas.unizar.es">fis@listas.unizar.es</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Fis] Fis Digest, Vol 10, Issue 11<br>
</div>
<div><br>
</div>
<div>
<div>
<div dir="ltr"><span style="font-size:13px">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? </span>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px">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.</div>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px">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. </div>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px">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. </div>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px">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.</div>
<div style="font-size:13px"><br>
</div>
<div style="font-size:13px">Jeremy Sherman</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Jan 17, 2015 at 5:06 AM, Moisés André Nisenbaum <span dir="ltr">
<<a href="mailto:moises.nisenbaum@ifrj.edu.br" target="_blank">moises.nisenbaum@ifrj.edu.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi, Pedro.
<div>I didnt receive th image (Figure 1. The Four Great Domains of Science)</div>
<div>Would you please send it again?</div>
<div><br>
</div>
<div>Thank you.</div>
<div><br>
</div>
<div>Moises</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2015-01-17 9:00 GMT-02:00 <span dir="ltr"><<a href="mailto:fis-request@listas.unizar.es" target="_blank">fis-request@listas.unizar.es</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: Beginnings and ends---Steps to a theory of reference &<br>
significance (Pedro C. Marijuan)<br>
<br>
<br>
---------- Mensagem encaminhada ----------<br>
From: "Pedro C. Marijuan" <<a href="mailto:pcmarijuan.iacs@aragon.es" target="_blank">pcmarijuan.iacs@aragon.es</a>><br>
To: "'fis'" <<a href="mailto:fis@listas.unizar.es" target="_blank">fis@listas.unizar.es</a>><br>
Cc: <br>
Date: Fri, 16 Jan 2015 12:43:40 +0100<br>
Subject: Re: [Fis] Beginnings and ends---Steps to a theory of reference & significance<br>
<u></u>
<div bgcolor="#ffffff" text="#000000">Dear Terry and FIS colleagues---and pirates,<small><br>
<br>
</small><big><small>Just a brief reflection on the below. </small><br>
<br>
</big>
<pre><small>(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.</small></pre>
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?
<br>
<br>
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?
<small><small><small><span style="font-family:Arial;color:black" lang="EN-US"></span></small></small></small>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.<br>
<br>
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".<br>
<br>
Thanks in advance for the patience!<br>
<br>
---Pedro<br>
<br>
<small><span style="font-family:Arial" lang="EN-US"><span style="color:black"></span></span></small><br>
<p class="MsoNormal" style="text-align:justify"><span style="font-family:Arial" lang="EN-US"><span style="color:black"></span></span></p>
<span style="font-family:Arial" lang="EN-US"><span style="color:black"> <u></u><u></u></span></span>
<p class="MsoNormal" style="text-align:center" align="center"><b><span style="font-family:Arial" lang="EN-US"><img height="386" width="424"><u></u><u></u></span></b></p>
<br>
<p class="MsoNormal" style="text-align:justify"><big><big><big><big><big><b><span style="font-size:9pt;line-height:115%;font-family:Arial;color:black" lang="EN-US">Figure 1. The Four Great Domains of Science</span></b><span style="font-size:9pt;line-height:115%;font-family:Arial;color:black" lang="EN-US">.
The graphic shows the network of contemporary disciplines in the background; <br>
while the superimposed “four-leaf clover” represents the four great scientific domains.<u></u><u></u></span></big></big></big></big></big></p>
<br>
<br>
<pre cols="72">--
-------------------------------------------------
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. <a href="tel:%2B34%20976%2071%203526" value="+34976713526" target="_blank">+34 976 71 3526</a> (& 6818)
<a href="mailto:pcmarijuan.iacs@aragon.es" target="_blank">pcmarijuan.iacs@aragon.es</a><a href="http://sites.google.com/site/pedrocmarijuan/" target="_blank">http://sites.google.com/site/pedrocmarijuan/</a>
-------------------------------------------------
</pre>
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<span class="HOEnZb"><font color="#888888"><br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">
<div>
<div dir="ltr">Moisés André Nisenbaum<br>
Doutorando IBICT/UFRJ. Professor. Msc.<br>
Instituto Federal do Rio de Janeiro - IFRJ<br>
Campus Maracanã<br>
<a href="mailto:moises.nisenbaum@ifrj.edu.br" target="_blank">moises.nisenbaum@ifrj.edu.br</a></div>
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