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 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, 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 individuals, brain organization, cellular
> >   processes, biomolecules) and how a myriad of information flows are
> >   crisscrossing, ascending, descending, focusing, mixing and
> >   controlling energy flows, etc. we may have an inkling that this
> >   evanescent world paradoxically becomes the master of the physical
> >   world (the "fluff" versus the "stuff", Lanham 2006), and that is
> >   organized far beyond the rules of the micro-macro-physical world.
> >   But how? What are the essentials of this magnificent "castle in the
> >   air" (reminding Escher's engrave: http://fis.sciforum.net/ )?
> >
> >   In next exchanges I will try to ad some more specifics on the above
> >   "fluffy" comments, derided from a fast reading of the Essay. Thanks
> >   again, Terry, for providing us this discussion opportunity in the
> >   New Year.
> >
> >   best  ---Pedro
> >
> >
> >
> > --
> > Professor Terrence W. Deacon
> > University of California, Berkeley
> >
> > --
> > -------------------------------------------------
> > 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.i...@aragon.es
> > http://sites.google.com/site/pedrocmarijuan/
> > -------------------------------------------------
> >
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