Re: [Fis] [Fwd: Re: Steps to a theory of reference significance] Terry Deacon

2015-01-09 Thread Guy A Hoelzer
Hi Terry,

I have a question about your ‘PS’.  I think of MEP as being constrained by 
potentials and a limited set of material opportunities (the adjacent 
possibilities).  I think of it as a thermodynamic version of natural selection 
in which some alternative states are thermodynamically favored over others, but 
this does not guarantee that dissipation will proceed to completion or that the 
particular alternative that absolutely generates the most efficient or 
effective dissipation will always be the manifested outcome (if there are a 
number of similarly optimal paths available).  Contingency on idiosyncratic 
configurations within and in the neighborhood of a system might lead the system 
to follow a variety of alternative paths.  Would you argue that autogenesis is 
not an MEP process from this somewhat fuzzy perspective?

Cheers,

Guy

Guy Hoelzer, Associate Professor
Department of Biology
University of Nevada Reno

Phone:  775-784-4860
Fax:  775-784-1302
hoel...@unr.edu

 On Jan 9, 2015, at 3:35 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es 
 wrote:
 
 Message from Terry Deacon
 
  Original Message 
 Subject:  Re: [Fis] Steps to a theory of reference  significance
 Date: Fri, 9 Jan 2015 03:32:22 +0100
 From: Terrence W. DEACON dea...@berkeley.edu
 To:   Pedro C. Marijuan pcmarijuan.i...@aragon.es
 References:   54ad3798.7060...@aragon.es 54ae7ca4.9080...@aragon.es
 
 
 
 This very brief reply should be routed to the FIS list please...
 
 One response: My choice of autogenesis is motivated by ...
 1. It is the simplest dynamical system I have been able to imagine that 
 exhibits the requisite properties required for an interpretive system (i.e. 
 one that can assign reference and significance to a signal due to intrinsic 
 properties alone - that is these features are independent of any extrinsic 
 perspective). A simple organism is far too complex. As a result it is 
 possible to make misleading assumptions about what we don't account for 
 (allowing us to inadvertently sneak in assumptions about what information is 
 and is not - for example just assuming that DNA molecule are intrinsically 
 informational). As I note when introducing this model, developing a simplest 
 but not too simple model system is the key to devising clear physical 
 principles.
 2. Autogenesis is not the same as autopoiesis (which is only a description of 
 presumed requirements for life) rather autogenesis is a well-described 
 empirically testable molecular dynamic, that is easily model able in all 
 aspects. Autopoiesis fit with the class of models assuming that simple 
 autocatalysis is sufficient and then simply adds (by assertion) the 
 (non-realized) assumption that autopoiesis can somehow be causally closed and 
 unitary, whereas in fact autocatalytic systems are intrinsically dissipative* 
 and subject to error catastrophe. More importantly, the assumption about 
 coherent finite unity and internal synergy is the critical one, and so it 
 needs to be the one feature that is explicitly modeled in order to understand 
 these aspects of information. 3. The self-regulating self-repairing 
 end-directed dynamic of autogenesis provides a disposition to preserve a 
 reference target state (even when its current state is far from it). This 
 serves as the necessary baseline for comparative assessment, without which 
 reference and significance cannot be defined because these are intrinsically 
 relativistic informational properties (there is a loose analogy here to the 
 3rd law of thermodynamics and the relativistic nature of thermodynamic 
 entropy).
 
 * PS: Autogenesis is also not a Maximim Entropy Production process because it 
 halts dissipation before its essential self-preserving constraints are 
 degraded and therefore does not exhaust the gradient(s) on which its 
 persistence depends.
 
 — Terry
 
 On Thu, Jan 8, 2015 at 1:48 PM, Pedro C. Marijuan pcmarijuan.i...@aragon.es 
 mailto:pcmarijuan.i...@aragon.es wrote:
 
   Dear Terry and colleagues,
 
   Thanks a lot for the opening text! It is a well crafted Essay full
   of very detailed contents. My impression is that the microphysics
   of information has been solved elegantly --at least at the level of
   today's relevant knowledge-- with your work and the works of related
   authors, one of them Karl Friston, who could be linked as a
   complementary approach to yours (in particular his recent Life as
   we know it, Royal Society Interface Journal, 10: 20130475). His
   Bayesian approach to life's organization, coupled with (variational)
   free energy minimization principle, conduces to the emergence of
   homeostasis and a simple form of autopoiesis, as well as the
   organization of perception/action later on. Thus, quite close to
   your approach on autogenic systems. About the different sections of
   the Essay, the very detailed points you deal with in section 4
   (steps to a formalization of reference)  are, 

[Fis] Response to Pedro's first comments:

2015-01-09 Thread Terrence W. DEACON
Response to Pedro's first comments: My choice of autogenesis is motivated
by ...
1. It is the simplest dynamical system I have been able to imagine that
exhibits the requisite properties required for an interpretive system (i.e.
one that can assign reference and significance to a signal due to intrinsic
properties alone - that is these features are independent of any extrinsic
perspective). A simple organism is far too complex. As a result it is
possible to make misleading assumptions about what we don't account for
(allowing us to inadvertently sneak in assumptions about what information
is and is not - for example just assuming that DNA molecule are
intrinsically informational). As I note when introducing this model,
developing a simplest but not too simple model system is the key to
devising clear physical principles.
2. Autogenesis is not the same as autopoiesis (which is only a description
of presumed requirements for life) rather autogenesis is a well-described
empirically testable molecular dynamic, that is easily model able in all
aspects. Autopoiesis fit with the class of models assuming that simple
autocatalysis is sufficient and then simply adds (by assertion) the
(non-realized) assumption that autopoiesis can somehow be causally closed
and unitary, whereas in fact autocatalytic systems are intrinsically
dissipative* and subject to error catastrophe. More importantly, the
assumption about coherent finite unity and internal synergy is the critical
one, and so it needs to be the one feature that is explicitly modeled in
order to understand these aspects of information.
3. The self-regulating self-repairing end-directed dynamic of autogenesis
provides a disposition to preserve a reference target state (even when its
current state is far from it). This serves as the necessary baseline for
comparative assessment, without which reference and significance cannot be
defined because these are intrinsically relativistic informational
properties (there is a loose analogy here to the 3rd law of thermodynamics
and the relativistic nature of thermodynamic entropy).

* PS: Autogenesis is also not a Maximim Entropy Production process because
it halts dissipation before its essential self-preserving constraints are
degraded and therefore does not exhaust the gradient(s) on which its
persistence depends.

— Terry

-- 
Professor Terrence W. Deacon
University of California, Berkeley
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[Fis] RV: Response to Pedro's first comments. --Bob Ulanowicz

2015-01-09 Thread PEDRO CLEMENTE MARIJUAN FERNANDEZ
Message from Bob Ulanowicz

De: Robert E. Ulanowicz [u...@umces.edu]
Enviado el: viernes, 09 de enero de 2015 19:30
Para: fis@listas.unizar.es
Asunto: Re: [Fis] Response to Pedro's first comments:

Terry Deacon wrote:

 3. The self-regulating self-repairing end-directed dynamic of autogenesis
 provides a disposition to preserve a reference target state (even when its
 current state is far from it). This serves as the necessary baseline for
 comparative assessment, without which reference and significance cannot be
 defined because these are intrinsically relativistic informational
 properties (there is a loose analogy here to the 3rd law of thermodynamics
 and the relativistic nature of thermodynamic entropy).

I think Terry does us a service by invoking the Third Law. We often forget
that information and entropy (complementarities) are both necessarily
relative to a reference distribution. What Terry's Autogen does is
establish an *extrinsic* reference point, which is helpful in maintaining
homeostasis.

I'll just remark that internal reference is possible as well. For example,
when Rutledge et al. (J. Theor. Biol. 57:355-371) applied IT to weighted
digraphs, they accomplished a stroke of genius by comparing the
distribution of outputs from each node to the corresponding distribution
of inputs into the *same* set of nodes. Thereby the self-referential
mutual information that results quantifies the organization intrinsic to
the network. None of the formalities of communication theory need be
invoked.

Unlike with Autogen, there is no halting to this process. When applied to
an autocatalytic set of processes, internal self-selection of nodes and
properties ensues that tends to increase the mutual information of the
system. Bertrand Russell saw in this tendency towards self-organization
(and the concomitant centripetality it induces) the primary drive for
evolution.

Even though self-reference is not extrinsic, it nonetheless can function
as an asymmetric form of homeostasis. If any disturbance occurs which
decreases mutual information (organization), the natural tendency is to
push the system back in the direction from which it was disturbed. If it
returns near to its undisturbed state, one can call this healing. If it
goes towards to different but survivable (or even more propitious) state,
then evolution has occurred.

Best to all,
Bob

-
Robert E. Ulanowicz|  Tel: +1-352-378-7355
Arthur R. Marshall Laboratory  |  FAX: +1-352-392-3704
Department of Biology  |  Emeritus, Chesapeake Biological Lab
Bartram Hall 110   |  University of Maryland
University of Florida  |  Email u...@umces.edu
Gainesville, FL 32611-8525 USA |  Web http://www.cbl.umces.edu/~ulan
--


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Re: [Fis] [Fwd: Re: Steps to a theory of reference significance] Terry Deacon

2015-01-09 Thread Terrence W. DEACON
Hi Guy,

Yes. Clearly self-organized dissipative processes can be blocked from
completely dissipating or else autogenesis could not be possible. The key
point is this: self-organized dissipative systems like tornados, growing
snow crystals, or Benárd convection cells do not involve any dynamical
features that intrinsically block rate increase to the point of maximizing
entropy production *within the given boundary constratints.* But this
starred phrase is the critical caveat. This is because Maximum Entropy
Production (MEP) must always be defined as a function of boundary
conditions, or as you might say available dissipation paths. This is true
for both of the component self-organized dynamics constituting simple
autogenesis (i.e. reciprocal catalysis and self-assembly) considered in
isolation. But when these are coupled, as in autogenesis, each becomes a
boundary condition for the other, both facilitating and limiting MEP of the
other. For each process considered alone there is no intrinsic MEP
limiting-regulating principle at work, but for the complex there is. And
this is a dynamical constraint that IS intrinsic to the system dynamics,
not an extrinsic boundary condition. This is why I would argue that living
organisms and life in general cannot be fully described in MEP terms alone.
Living processes build constraints utilizing self-organized processes but
which are reciprocally prevented from fully dissipating. They therefore
reciprocally *regulate* entropy production rate rather than let the process
run to maximum. I would argue, for example, that life on earth has been
continually (until the last couple of centuries) sequestering energy-rich
molecules (e.g. fossil fuels, etc.) rather than helping that captured solar
radiation to more rapidly escape into space. This offers a challenge to a
theory (MEPP) that has recently been heralded as a key to explaining life.
But it does not violate the basic logic of far-from-equilibrium
thermodynamics. It is  rather a further development, that now includes a
non-linear factor: dissipative processes that collectively produce and
modify their own boundary conditions. But as with the introduction of an
such nonlinearity this can produce some quite unexpected emergent
consequences. This is what makes the dynamic that we call life so radically
different in what it can do compared to non-living dissipative dynamics.

To demonstrate that this sort of nonlinearity is not weirdly divergent from
standard theory I often use the following somewhat oversimplified and not
uncommon thermodynamic example to show how a process of increasing entropy
dissipation can be its own self-limiter.

Consider convection through a tall building with an open door on the ground
floor and an open window on an upper floor and heat convection causing
airflow in from the door and out from the window. Now additionally, imagine
that the window opens inward but only part way. So long as the convection
flow is below a certain threshold it will increase in rate thus
progressively increasing dissipation. But when it reaches a flow rate that
is strong enough to blow the window closed it stops all dissipation. Though
this is not intrinsic dynamical regulation as in autogenesis, in
combination with the mechanics of the window and the capacity of the
convection gradient to do mechanical work to alter this boundary condition
we can see that for the very reason that dissipative processes have the
capacity to do work to alter coupled systems there can be interesting
nonlinearities to even simple dissipative systems. This should not be
mysterious. but it does suggest that we may need to modify claims that life
is merely an entropy maximizing process.

— Terry

On Fri, Jan 9, 2015 at 7:59 PM, Guy A Hoelzer hoel...@unr.edu wrote:

 Hi Terry,

 I have a question about your ‘PS’.  I think of MEP as being constrained by
 potentials and a limited set of material opportunities (the adjacent
 possibilities).  I think of it as a thermodynamic version of natural
 selection in which some alternative states are thermodynamically favored
 over others, but this does not guarantee that dissipation will proceed to
 completion or that the particular alternative that absolutely generates the
 most efficient or effective dissipation will always be the manifested
 outcome (if there are a number of similarly optimal paths available).
 Contingency on idiosyncratic configurations within and in the neighborhood
 of a system might lead the system to follow a variety of alternative
 paths.  Would you argue that autogenesis is not an MEP process from this
 somewhat fuzzy perspective?

 Cheers,

 Guy

 Guy Hoelzer, Associate Professor
 Department of Biology
 University of Nevada Reno

 Phone:  775-784-4860
 Fax:  775-784-1302
 hoel...@unr.edu

  On Jan 9, 2015, at 3:35 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es
 wrote:
 
  Message from Terry Deacon
 
   Original Message 
  Subject:  Re: [Fis] Steps to a theory 

[Fis] MEPP

2015-01-09 Thread Stanley N Salthe
TD: Autogenesis is also not a Maximum Entropy Production process because it
halts dissipation before its essential self-preserving constraints are
degraded and therefore does not exhaust the gradient(s) on which its
persistence depends.


S: Abiotic dissipative structures will degrade their gradients as fast as
possible given the bearing constraints. They are unconditional maximizers.
Life that has survived has been able to apply conditions upon its entropy
production, but that does not mean that it has enacted energy conservation
or energy efficiency policies.  Its mode is still maximizing, but within
limits.


GH: I think of [MEPP] as a thermodynamic version of natural selection in
which some alternative states are thermodynamically favored over others,
but this does not guarantee that dissipation will proceed to completion or
that the particular alternative that absolutely generates the most
efficient or effective dissipation will always be the manifested outcome
(if there are a number of similarly optimal paths available).  Contingency
on idiosyncratic configurations within and in the neighborhood of a system
might lead the system to follow a variety of alternative paths.


S: I think that the keyword here is ‘striving’  Living things are mostly
always striving, so they reach for the maximum until it ‘hurts’.


GH: Would you argue that autogenesis is not an MEP process from this
somewhat fuzzy perspective?


TD:  This offers a challenge to a theory (MEPP) that has recently been
heralded as a key to explaining life. But it does not violate the basic
logic of far-from-equilibrium thermodynamics. It is  rather a further
development, that now includes a non-linear factor: dissipative processes
that collectively produce and modify their own boundary conditions. But as
with the introduction of an such nonlinearity this can produce some quite
unexpected emergent consequences. This is what makes the dynamic that we
call life so radically different in what it can do compared to non-living
dissipative dynamics.


This -snip- does suggest that we may need to modify claims that life is
merely an entropy maximizing process.


S: I think no one has argued that living systems are ‘merely’ entropy
production maximizers. That might be the view of the Universe, if it could
have a view. But finalities can be parsed as {entropy production {free
energy dissipation {work}}} on the template {physical process {chemical
actions {living activity}}}.  At each level we have finalities {Second Law
{Maupertuis’ least energy {goal seeking}}}. The outermost class is locally
the weakest impulse, but it acts continuously and ‘fills in’ immediately
there is any hesitation, while the innermost subclass is the most
immediately effective, but its enthusiasms come and go, and do not last.


STAN
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[Fis] Section 4/Re: Steps to a theory of reference significance

2015-01-09 Thread Pedro C. Marijuan
(Following some requests, I include herewith the points of Section 4, 
the theoretical core.
For recent subscribers--some pirates on board!-- the responses should 
directly go to: fis@listas.unizar.es
Also, remember please that only two messages per week are allowed, 
except the discussion chair, Terry, and my own maintenance work. For 
instance, as a regular discussant I have only one shot left to respond 
to Terry and Jeremy...  
best---Pedro)*

---
_
Steps to a theory of reference  significance in information_
*FIS discussion paper by Terrence W. Deacon (2015)*

[Section 4] Steps to a formalization of reference:*

A. General case: passive information medium near equilibrium [ e.g. 
geological formation, crime

scene evidence, data from a scientific experiment, text, etc.]

1. Information (e.g. Shannon) entropy is NOT equivalent to thermodynamic 
(e.g. Boltzmann-
Gibbs) entropy (or to the absolute statistical diversity of physical 
states). [For convenience
these entropies will be provisionally distinguished as Shannon versus 
Boltzmann entropy,

though recognizing that each includes multiple variant forms.]

2. However, for any physical signal medium, a change in Shannon entropy 
must also
correspond to a change in Boltzmann entropy, though not vice versa 
because the distinctions
selected/discerned to constitute the Shannon entropy of a given signal 
medium are typically a
small subset of the possible physical variety of states---e.g. 
statistical entropy---of that

medium. (See notes below.).

3a. The Shannon information of a received message is measured as a 
reduction of signal

uncertainty (= a reduction of Shannon entropy).
3b. For a simple physical medium reduction of Shannon entropy must also 
correspond to a

reduction of the Boltzmann entropy of that medium.
3c. This can be generalized as any deviation away from a more probable 
state (which can
violate 3b in the case of media that are actively maintained in an 
improbable state, such as

maintained far-from-equilibrium. See B below.).

4a. A reduction of Boltzmann entropy of any physical medium is exhibited 
as constraint on its

possible states or dynamical trajectories.
4b. The production of physical constraint requires physical work in 
order to produce a decrease

of Boltzmann entropy, according to the 2nd law of thermodynamics.

5a. For a passive medium the physical work required to reduce its 
Boltzmann entropy must

originate from some physical source extrinsic to that medium.
5b. Generalization: Constraint of the Shannon entropy of a passive 
medium = constraint of its

Boltzmann entropy = the imposition of prior work from an external source.

6. An increase in constraint (i.e. deviation away from a more probable 
state) in the information
medium literally re-presents the physical relationship between the 
medium and the
extrinsic contextual factors (work) that caused this change in entropy. 
(= what the information embodied

in the constraint can be about.)

7. Since a given constraint has statistical structure, its form is a 
consequence of the specific
structure of the work that produced it, the physical susceptibilities of 
the information bearing
medium, and the possible/probable physical interactions between that 
medium and this

extrinsic contextual factor.

8. The form of this medium constraint therefore corresponds to and can 
indirectly re-present

the form of this work. (i.e. in-form-ation)

9. Conclusion 1. The possibility of reference in a passive medium is a 
direct reflection of the
possibility of a change in the Boltzmann and Shannon entropies of that 
medium due to a
physical interaction between the information bearing medium and a 
condition extrinsic to it.


10. Conclusion 2. The possible range of contents thereby referred to is 
conveyed by the form of
the constraint produced in the medium by virtue of the form of work 
imposed from an

extrinsic physical interaction.

11. Conclusion 3. The informing power of a given medium is a direct 
correlate of its capacity to

exhibit the effects of physical work with respect to some extrinsic factor.

12. Corollary 1. What might be described as the referential entropy of a 
given medium is a
function of the possible independent dimensions of kinds of 
extrinsically induced physical
modifications it can undergo (e.g. physical deformation, electromagnetic 
modification, etc.)
multiplied by the possible distinguishable (see notes) states within 
each of these

dimensions.

13. Corollary 2. Having the potential to exhibit the effects of work 
with respect to some extrinsic
physical factor means that even no change in medium entropy or being in 
a most probable
state still can provide reference (e.g. the burglar alarm that has not 
been tripped, or the failure
of an experimental intervention to make a difference). It is thus 
reference to the fact that no

work to change the 

Re: [Fis] Steps to a theory of reference significance

2015-01-09 Thread Jeremy Sherman
Hi Pedro,

Jeremy Sherman here, a long-time pirate. Pleased to meet you. You say:

I am also critical with the autogenesis model systems--wouldn't it be far
clearer approaching a (relatively) simple prokaryotic cell and discuss upon
its intertwining of the communication and self-production arrangements? The
way a bacterium sees the world, and reorganizes its living, could be a
very useful analysis. I think it leads to a slightly different outcome
regarding reference/significance, and meaning/value/fitness.

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 explanan.

Somewhat related, I recently came across this:

*Epistemological particularism* is the belief that one can know something
without knowing how one knows that thing.[1]
http://en.wikipedia.org/wiki/Epistemological_particularism#cite_note-1 By
this understanding, one's knowledge is justified before one knows how such
belief could be justified. Taking this as a philosophical approach, one
would ask the question What do we know? before asking How do we know?
The term appears in Roderick Chisholm
http://en.wikipedia.org/wiki/Roderick_Chisholm's The Problem of the
Criterion http://en.wikipedia.org/wiki/Problem_of_the_Criterion, and in
the work of his student, Ernest Sosa
http://en.wikipedia.org/wiki/Ernest_Sosa (The Raft and the Pyramid:
Coherence versus Foundations in the Theory of Knowledge). Particularism is
contrasted with Methodism
http://en.wikipedia.org/wiki/Methodism_(philosophy), which answers the
latter question before the former. Since the question What do we know
implies that we know, particularism is considered fundamentally
anti-skeptical, and was ridiculed by Kant
http://en.wikipedia.org/wiki/Immanuel_Kant in the*Prolegomena
http://en.wikipedia.org/wiki/Prolegomena*.

We Pirates do what we can to stay on the epistemological methodist side of
things.

Even the simplest prokaryotic cell is extraordinarily complex. We don't
want to run before we can walk.  The briskest runners-before-walkers are
those who want to go straight from physics to human consciousness, a leap
that we think makes the endeavor thoroughly intractable.

Best,

Jeremy

On Thu, Jan 8, 2015 at 4:48 AM, Pedro C. Marijuan pcmarijuan.i...@aragon.es
 wrote:

 Dear Terry and colleagues,

 Thanks a lot for the opening text! It is a well crafted Essay full of very
 detailed contents. My impression is that the microphysics of information
 has been solved elegantly --at least at the level of today's relevant
 knowledge-- with your work and the works of related authors, one of them
 Karl Friston, who could be linked as a complementary approach to yours (in
 particular his recent Life as we know it, Royal Society Interface
 Journal, 10: 20130475). His Bayesian approach to life's organization,
 coupled with (variational) free energy minimization principle, conduces
 to the emergence of homeostasis and a simple form of autopoiesis, as well
 as the organization of perception/action later on. Thus, quite close to
 your approach on autogenic systems. About the different sections of the
 Essay, the very detailed points you deal with in section 4 (steps to a
 formalization of reference)  are, in my opinion, the  conceptual core and
 deserve a careful inspection, far more than these rushed comments. In any
 case, the relationship Boltzmann-Shannon entropies has been cleared quite
 elegantly.

 However, for my taste the following sections have not sufficiently opened
 the panorama. And with this I start some critical appreciations. Perhaps
 the microphysics of information is not the critical stumbling block to me
 removed for the advancement of the informational perspective. We could
 remain McLuhan's stance on Shannon's information theory and von Neumann's
 game theory... yes, undoubtedly important advancements, but not the
 essential stuff of information. But in this list there are people far more
 versed in McLuhan's contents and whether the caveats he raised would
 continue to apply (obviously in a different way). I am also critical with
 the autogenesis model systems--wouldn't it be far clearer approaching a
 (relatively) simple prokaryotic cell and discuss upon its intertwining of
 the communication and self-production arrangements? The way a bacterium
 sees the world, and reorganizes its living, could be a very useful
 analysis. I think it leads to a slightly different outcome regarding
 reference/significance, and meaning/value/fitness.

 If we look at the whole view of the information world (human societies,
 behaving 

[Fis] [Fwd: Re: Steps to a theory of reference significance] Terry Deacon

2015-01-09 Thread Pedro C. Marijuan

Message from Terry Deacon

 Original Message 
Subject:Re: [Fis] Steps to a theory of reference  significance
Date:   Fri, 9 Jan 2015 03:32:22 +0100
From:   Terrence W. DEACON dea...@berkeley.edu
To: Pedro C. Marijuan pcmarijuan.i...@aragon.es
References: 54ad3798.7060...@aragon.es 54ae7ca4.9080...@aragon.es



This very brief reply should be routed to the FIS list please...

One response: My choice of autogenesis is motivated by ...
1. It is the simplest dynamical system I have been able to imagine that 
exhibits the requisite properties required for an interpretive system 
(i.e. one that can assign reference and significance to a signal due to 
intrinsic properties alone - that is these features are independent of 
any extrinsic perspective). A simple organism is far too complex. As a 
result it is possible to make misleading assumptions about what we don't 
account for (allowing us to inadvertently sneak in assumptions about 
what information is and is not - for example just assuming that DNA 
molecule are intrinsically informational). As I note when introducing 
this model, developing a simplest but not too simple model system is the 
key to devising clear physical principles.
2. Autogenesis is not the same as autopoiesis (which is only a 
description of presumed requirements for life) rather autogenesis is a 
well-described empirically testable molecular dynamic, that is easily 
model able in all aspects. Autopoiesis fit with the class of models 
assuming that simple autocatalysis is sufficient and then simply adds 
(by assertion) the (non-realized) assumption that autopoiesis can 
somehow be causally closed and unitary, whereas in fact autocatalytic 
systems are intrinsically dissipative* and subject to error catastrophe. 
More importantly, the assumption about coherent finite unity and 
internal synergy is the critical one, and so it needs to be the one 
feature that is explicitly modeled in order to understand these aspects 
of information. 
3. The self-regulating self-repairing end-directed dynamic of 
autogenesis provides a disposition to preserve a reference target state 
(even when its current state is far from it). This serves as the 
necessary baseline for comparative assessment, without which reference 
and significance cannot be defined because these are intrinsically 
relativistic informational properties (there is a loose analogy here to 
the 3rd law of thermodynamics and the relativistic nature of 
thermodynamic entropy).


* PS: Autogenesis is also not a Maximim Entropy Production process 
because it halts dissipation before its essential self-preserving 
constraints are degraded and therefore does not exhaust the gradient(s) 
on which its persistence depends.


— Terry

On Thu, Jan 8, 2015 at 1:48 PM, Pedro C. Marijuan 
pcmarijuan.i...@aragon.es mailto:pcmarijuan.i...@aragon.es wrote:


   Dear Terry and colleagues,

   Thanks a lot for the opening text! It is a well crafted Essay full
   of very detailed contents. My impression is that the microphysics
   of information has been solved elegantly --at least at the level of
   today's relevant knowledge-- with your work and the works of related
   authors, one of them Karl Friston, who could be linked as a
   complementary approach to yours (in particular his recent Life as
   we know it, Royal Society Interface Journal, 10: 20130475). His
   Bayesian approach to life's organization, coupled with (variational)
   free energy minimization principle, conduces to the emergence of
   homeostasis and a simple form of autopoiesis, as well as the
   organization of perception/action later on. Thus, quite close to
   your approach on autogenic systems. About the different sections of
   the Essay, the very detailed points you deal with in section 4
   (steps to a formalization of reference)  are, in my opinion, the 
   conceptual core and deserve a careful inspection, far more than

   these rushed comments. In any case, the relationship
   Boltzmann-Shannon entropies has been cleared quite elegantly.

   However, for my taste the following sections have not sufficiently
   opened the panorama. And with this I start some critical
   appreciations. Perhaps the microphysics of information is not the
   critical stumbling block to me removed for the advancement of the
   informational perspective. We could remain McLuhan's stance on
   Shannon's information theory and von Neumann's game theory... yes,
   undoubtedly important advancements, but not the essential stuff of
   information. But in this list there are people far more versed in
   McLuhan's contents and whether the caveats he raised would continue
   to apply (obviously in a different way). I am also critical with the
   autogenesis model systems--wouldn't it be far clearer approaching a
   (relatively) simple prokaryotic cell and discuss upon its
   intertwining of the communication and self-production arrangements?
   The way a bacterium sees the world,