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Dynamic constraint based phenomena

Summary
Terrence Deacon explores how constraints on dynamic flows can induce emergent phenomena which can do real work.  He shows how these phenomena are sustained.  The mechanism enables the development of
This page reviews the implications of selection, variation and heredity in a complex adaptive system (CAS).  The mechanism and its emergence are discussed. 
Darwinian competition

Incomplete Nature
Terrence Deacon's book 'Incomplete Nature' is structured as four parts:
  1. The problem of end-directedness
  2. Problems with previous approaches to explaining end-directedness. 
  3. Deacon's alternative approach
  4. Applying Deacon's approach to enable an expanded science.  
End-directedness
Deacon introduces a number of benefits and problems of end-directedness.  The functional design of living things appears well matched to the task of survival, competition and reproduction.  But explaining how the end-directed functional designs were achieved has been difficult.  The end-directed nature seems to imply some purpose to existence and the presence of a designer.  The conscious mind seems to peer from within us.  The nature of these functions, values, information, purposes and references appeared ill-defined and incomplete. 
Problems of previous approaches
Deacon sees merit in the study of failed approaches which he asserts can highlight what to avoid in a replacement strategy.

Deacon reviews a number of historic and currently used approaches to explaining or coping with the existence of end-directedness.  His classes of approaches are: homunculi, golems, teleonomy and emergence;

Homunculi
Deacon demonstrates that history is littered with explanations of end-directedness which depend on a designer.  But the possibility of creation by a higher being results in a recursive trap.  Who created the creator?  Teleology identifies an origin, but could not provide a mechanism for the operation of the origin.  When science becomes able to explain the mechanism it has eliminated the need for the teleological logic. 

Golems
Deacon argues that a second approach is to ignore the designer and his end-directed effects.  Scientists unhappy with the nature of recursive self-reference, dualism and creationism have focused their studies on material aspects of systems.  They adopted methodologies which ignore end-directed phenomena, or identify them as place-holders to be replaced with physical or statistical mechanisms. 

Unfortunately, this approach limits the scope of scientific research and can result in confusion.  By ignoring sources of final cause scientists do not apply the scientific method to end-directedness.  As such the domain remains mysterious.  No scientific models or methods are expanded to account for the effects. 

When science has misdiagnosed these phenomena the failures remain, and can introduce confusion.  Deacon outlines how DNA (DNA), a polymer composed of a chain of deoxy ribose sugars with purine or pyrimidine side chains.  DNA naturally forms into helical pairs with the side chains stacked in the center of the helix.  It is a natural form of schematic string.  The purines and pyrimidines couple so that AT and GC pairs make up the stackable items.  A code of triplets of base pairs (enabling 64 separate items to be named) has evolved which now redundantly represents each of the 20 amino-acids that are deployed into proteins, along with triplets representing the termination sequence.  Chemical modifications and histone binding (chromatin) allow cells to represent state directly on the DNA schema.  To cope with inconsistencies in the cell wide state second messenger and evolved amplification strategies are used. 
has been viewed as a recipe, and a blue-print.  But neither model advances a mechanism for how DNA emerged as a source of information controlling evolution, or explains the nature of that information.  End-directed properties of the
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organism
are associated with the DNA without explanation of the process involved.  Natural Selection results in the emergence of ententional phenomena.  But scientific explanations have been limited.  Information has been viewed as shorthand for true mechanistic operations. 

Chomsky argued language was based on a deep grammar.  But what interprets this grammar? 

Artificial intelligence aims to use large numbers of stupid machines to create intelligence mechanistically.  But algorithms are programmed by human programmers, to operate according to their designs.  IBM's chess playing computer Deep Blue extends this approach including applying Bayesian is an iterative form of statistics invented by Thomas Bayes.  It uses a 'prior' statistic to represent the prior situation and then performs a calculation that integrates the probability of new events occurring into a 'posterior' probability.  This posterior becomes the prior for the next iteration with the application of the Bayesian identity xpost = xprior*y/(xprior*y + z(1-xprior)).  The magic in Bayesian statistics is in accurately generating the prior xprior and the current event probabilities y and z.  R. A. Fischer was so skeptical of the legitimacy of the prior that he advocated an alternative statistical framework and experimental process.   statistics to Internet data.  Again any intelligence seems to be provided by the Deep Blue designers and creators of the Internet data. 

Teleonomy
Deacon describes Teleonomy, which by only specifying the way a mechanistic process can be organized so that it converges toward a specific state, rather than behavior for the sake of an end.  This conception avoided sneaking mentalistic assumptions about teleology back into biological design. 

If evolution can also be understood as nothing more than retained and reproduced accidental organization then end-directedness can be reasonably viewed as mechanistic.  But Deacon argues that Teleonomy's mechanism agnosticism just hides the existence of the end-directedness.  The mechanistic programs are still designed by humans.  He is concerned that natural selection includes replication which is a self-referential loop. 

Consequently Deacon asks 'What kind of system properties are required to transform a mere physical pattern embedded within that system into information that is both able to play a constitutive role in determining the organization of this system and constraining it to be capable of self-generation, maintenance and reproduction in its local environment?' 

Additionally Deacon argues reproduction and generation of
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organism
forms are necessary requirements for Darwin's evolutionary logic, even though how this is accomplished is largely irrelevant to the existence of natural selection's consequences.  This disconnect makes the process non-teleological.  But natural selection depends on lower layer ententional properties.  These are not a product of natural selection even if preserved by it. 

What sort of physical process is necessary for evolution to take place and locally overcome the second law of thermodynamics requires that the Boltzmann entropy of a closed system increases. 
?  Besides the genetic string there must be a system to utilize and copy the pattern and itself, and a way to counter the thermodynamic degradation.  That necessitates specific molecular substrates, potential difference in energy to synthesize and drive reactions, work required to generate the structures and processes that get reproduced with variation.  Deacon notes that most computer based systems take the physics for granted, including the computer's physical architecture implicitly, and hence fail to represent the essential physical constraints of the real world. 

Emergence
By the mid-nineteenth century, a mechanistic and statistical approach to natural philosophy had begun to coalesce and displace the previously more teleological and platonic forms of explanation.  Deacon comments ... Nature's designs, including living and mental processes, were now viewed through the lens of materialism.  A methodology, reductionism, for analyzing nature's designs was adopted.  Decompose the whole into parts.  But what is a part is not always obvious.  Reductionism pulls the focus away from the contribution of the interaction complexity, M. Mitchell Waldrop describes a vision of complexity via:
  • Rich interactions that allow a system to undergo spontaneous self-organization
  • Systems that are adaptive
  • More predictability than chaotic systems by bringing order and chaos into
  • Balance at the edge of chaos 
within systems. 

Emergentists focused their attention toward the details of emergent functional properties.  Deacon outlines Roger Sperry's logic about a wheel having key translational properties which its disassembled components do not have. 

Two perspectives were developed by emergence researchers:
  1. Ontological - Emergence changes the causal landscape by introducing discontinuous functional properties. 
  2. epistemological - Discontinuities arise from our intrinsic inability to predict emergent properties from the lower level laws.  Non-linear features of chaotic systems illustrate this alternative.  
Deacon explains that Jaegwon Kim showed that if all higher-order causal interactions are between objects constituted by relationships among these ultimate building blocks of matter, then assigning causal power to various higher-order relations is redundant.  Deacon accepts that this totally undermines the ontological emergence of functionalism.  But he continues that our understanding of physics has not identified ultimate particles or simple atoms devoid of lower-level compositional organization.  Instead, he suggests, the particulate features of matter are statistical regularities of a dynamically unstable substrate. 

Deacon asserts that the dynamics are irreducibly process like and thus are by definition organized.  Following Mark Bickhard he argues if process organization is the irreducible source of the causal properties at a particular level, then it, to quote Bickhard, 'cannot be de-legitimated as a potential locus of causal power without eliminating causality from the world.'  Static notions of part and whole are for this reason suspect since the wholes we are interested in are dynamical and the parts are constantly in flux.  The parts are constantly being synthesized, damaged, and replaced, while the whole persists.  Deacon sees this framework as compatible with Stuart Kauffman's emergence work.  Deacon argues that once part/whole distinctions and their supervenience indicates that a high level property does not exist as and of itself but because lower level properties determine the higher level property, which Abbott views as epiphenomena.  Deacon argues that instead of supervenience relations Bickhard's dynamic processes allow the emergence of high level phenomena. 
relations are replaced by Bickhard's dynamic processes emergence of discontinuous properties becomes legitimate. 

Deacon's alternative approach - a process based mechanism of emergent dynamics and self-assembly
Deacon argues for an alternative scientific strategy which accepts the existence of end-directed phenomena.  He models how they emerge, and illustrates how the approach allows science improved access to key aspects of our world including: work, information, significance, evolution, self, sentience and consciousness

Constraints
Deacon's theory relies on the effects of constraints on flows.  Deacon views constraints as the physical characterization of a habit (a regularity of behavior) following Charles Peirce.  Peirce argued that emergence is instantiated as some form of realism with dynamic constraints.  This contrasts with Nominalists, such as Occam who viewed all universals as mental groupings mistakenly viewed as real based on specific individual instances.  As such Deacon aims to show how real physical effects emerge.  He outlines how constraints can:
  • Generate real classes of process based on exclusion.  The constraint removes any components from the process which do[n't] contain, particular properties.  This allows an emergent general class of dynamic process to exist based on exclusion of components with particular properties.  The objects in the class have not been assessed by any positive attribute.  Deacon writes 'The concept of constraint is, in effect, a complementary concept of order, habit and organization, because it determines a similarity class by exclusion.  Hence abstract properties do not have to have physical potency, but certain general properties can produce other general properties as causal consequences. ' ... 'If certain physical interactions also tend to drop out selective details, then there can also be a purely physical analogue to the abstraction process.'  And Deacon argues that constraint can also account for concrete abstractions since what something doesn't exhibit, it can't impose on something else via interaction.  To the extent that differences in one system can produce differences in the other, those variations not expressed in one will not be transferred to the other during their interaction.  It is precisely by virtue of what is not enabled, but could otherwise have occurred, that a change can be forced. 
  • Support the capacity to perform work.  
  • Appear as increased statistical likelihood.  With assent of scale micro effects typically average out, while highly constrained, and consequently stable, interactions become much more likely to be expressed in any interactions with other components. 
  • In massively componential dynamical systems where there is the possibility of extensive non-linear interactions (for example in systems persistently maintained far from equilibrium), constraints can amplify to become macroscopically expressed.  The emergence of new constraints at the macroscopic level can be a source of new forms of work. 
The effects of constraints are amplified by scale hierarchies.  Vast numbers of low level dynamics occur extremely rapidly, relative to higher level processes.  Averaging, and coherence effects tend to average out so that only generalized attractor features have causal influence at the higher level.  Conversely this means that reductionistic analysis cannot recover these differences. 

Deacon argues that constraint is relational to the other dynamic options.  States that are not realized or that occur only improbably in a given process can play the critical causal role in the formation of further constraints at higher levels. 

Deacon analyses both near equilibrium homeodynamic processes, and far from equilibrium dynamical conditions (morphodynamics and teleodynamics).

Only far from equilibrium conditions enable spontaneous change of macroscopic state.  When things change in non-spontaneous ways, they must be caused to do so extrinsically, by a force and through doing work.  Using fuel uses up its capacity to do work, but conserves the energy transforming it from one form to another more widely distributed form, and reducing the difference in the distribution of some quantity of some constrained physical property of the fuel. 

Homeodynamics
Our universe mostly consists of near equilibrium conditions.  Deacon's homeodynamics describes these conditions as generally as possible.  He distinguishes two contrasting dynamics (orthograde and contragrade) within any homeodynamic process. 

Orthograde dynamics
The second law of thermodynamics requires that the Boltzmann entropy of a closed system increases. 
is represented by Deacon's orthograde dynamics which reduce the spontaneous asymmetry of a constrained ('ordered') state to a less constrained ('disordered') state of dynamic change by filling the maximum number of microstates. 

Contragrade dynamics
The reverse direction of change (Deacon's contragrade process), which does not tend to occur spontaneously is a response to the imposition of highly constrained external work.  While the action of each component in the orthograde dynamic is fully reversible, the gross redistribution of microstates populated shifts irreversibly from the highly constrained towards the average.  The general applicability of the second law to our universe is due to the universe's deeply asymmetric predisposition concerning any process involving many components.  Contragrade change is the natural consequence of one orthograde process influencing (constraining) another orthograde process through some medium, each process in some way undoing the other's effects. 

Constraint and ortho/contragrade dynamics
Deacon redefines constraint in orthograde/contragrade terms.  Constraints are defined with respect to orthograde maxima (when orthograde dynamic change is no longer asymmetric).  A constrained orthograde process is one in which certain dimensions of change are not available.  This may be due to a barrier (wall) or a contragrade process countering the orthograde change.  A contragrade process at one level can generate conditions for a higher-level orthograde process of constraint generation

Deacon regards entropy as an inverse measure of constraint.  He argues that the dissociation of macro- from micro-processes that characterizes thermodynamic systems means that we cannot attribute the asymmetry of thermodynamic change to the properties of individual molecular collisions alone.  Molecular collisions are necessary for any change of state of a typical thermodynamic system, but they are not sufficient to determine its asymmetric direction of change.  This is ultimately due to the highly asymmetric 'geometry' of the possible distributions of molecular properties and trajectories of their movements. 

For Deacon homeodynamics, in comparison to thermodynamics, more generally describes the most basic orthograde dynamic.  It is a dynamic that spontaneously reduces constraints to their minimum and thus more evenly distributes (reduces asymmetry) whatever property is being changed.  He sees thermodynamic entropy increase as a more specific case of this focusing only on orthograde statistical mechanics.   In contrast Deacon highlights a key principle of general homeodynamics: orthograde and contragrade dynamics reverse in dominance in adjacent layers of process.  The special contragrade relationships that can be generated by the juxtaposition of different orthograde processes can produce complex forms of constraint.  For Deacon homeodynamics is thus the engine of emergence. 

In contrast to spontaneous homeodynamics Deacon's morphodynamics operates in far from equilibrium systems which do not occur spontaneously. 

Morphodynamics
Deacon views understanding the [morpho]dynamics of inorganic order-promoting processes as offering hints that can be carried forward into explorations of causality supporting life and mind. 

So long as extrinsic constraints are continually imposed, creating a contragrade dynamic to the spontaneous orthograde dissipation  of intrinsic constraints, new forms of intrinsic constraint can emerge and even amplify. 

Morphodynamics characterizes the dynamical organization of a diverse class of phenomena which share in common the tendency to become spontaneously more organized and orderly over time due to constant perturbation, but without the extrinsic imposition of influences that specifically impose the regularity (teleodynamics). 

W. Ross Ashby defined a self-organizing system as one that spontaneously reduces its entropy, but not necessarily its thermodynamic entropy, by reducing the number of its potential states.  Deacon argues functional complexity, M. Mitchell Waldrop describes a vision of complexity via:
  • Rich interactions that allow a system to undergo spontaneous self-organization
  • Systems that are adaptive
  • More predictability than chaotic systems by bringing order and chaos into
  • Balance at the edge of chaos 
and synergy of
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organisms
ultimately depends on Ashby's logic of self-simplification. 

Deacon explores a Benard cell (Rayleigh-Benard convection) as a morphodynamic exemplar.  He explains that there are intrinsic biases available (buoyancy differences, viscosity effects and geometric distribution constraints in this case).  The persistent imposition of constraint (constant heating) will tend to redistribute this additional constraint into the added dimensions of potential difference of the intrinsic biases.  The additional dimensions are boundary conditions.  Because the additional dimensions are system wide and ubiquitous they are on a higher level of scale than the constraints of molecular interaction.  The transfer of constraints from molecular-level differences to global-level differences also increase the propagation of constraint from lower- to higher-order dynamics. 

Deacon concludes these are common dynamic features that characterize morphodynamic phenomena, and make them an emergent level removed from subvenient homeodynamic processes whether at the thermodynamic or sub-atomic level.  In each case he explains we find a tangled hierarchy of causality, where micro-configurational particularities can be amplified to determine macro-configurational regularities.  Where these in turn further constrain and/or amplify subsequent cycles of this process, producing a compounding.  The special reflexive regularities and the recurrent causal architecture of the cycles of interaction have come to overshadow the system's lower-order orthograde properties.  These systems must be open to the flow of energy and/or components, which is what enables their growth and/or development, but they additionally include a higher order form of closure as well.  Such flows propagate constraints inherited from past states of the system, which recurrently compound to further constrain the future behavior of its components interactions.  Deacon continues 'The new higher-order orthograde dynamic that is created by this compounding of constraints is what defines and bounds the higher order of constraints that we identify as the system.  This centrality of form-begetting-form is what justifies calling these processes morphodynamic.  The generation of new orthograde dynamical regimes is what justifies describing morphodynamic processes as emergent from thermodynamic processes.' 

Teleodynamics
Deacon argues there is an additional emergent transition which is dynamically supervenient on morphodynamics and thermodynamics.  Morphodynamic processes generate order, but not representation or functional organization and they lack any normative (or evaluative) character because there is nothing like a self to benefit or suffer.  Deacon's teleodynamics has characteristic end-directedness and consequence-organized features. 

Living processes create protected local domains in which orthograde increase in entropy is effectively reversed by contragrade processes that generate order and new structural components at the expense of a net entropy increase in their surroundings.  Living processes persistently decrease entropy within themselves and their progeny over the course of evolution, by developing and evolving complex supportive correlations between structures and processes for maintaining bodies and ecosystems. 

Deacon regards evolutionary diversity as key.  He argues the most dramatic expression of the emergent nature of life's distinctive dynamic is the generation of increasingly diverse and complex forms of
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organisms
that have evolved during the past 3.5 billion years of Earth history and have adapted to an ever-increasing range of environmental conditions.  This process is spontaneous based on its dynamic asymmetry, and hence is orthograde.  The global asymmetric dynamic of evolution is only an indirect higher-order product of the work done by organisms resisting degradation long enough to reproduce.  It is the result of formal asymmetries in the space of options (niches) for adaptation in evolutionary biology is a trait that increased the number of surviving offspring in an organism's ancestral lineage.  In Deacon's conception of evolution an adaptation is the realization of a set of constraints on candidate mechanisms, and so long as these constraints are maintained, other features are arbitrary. 
that spontaneously arise over time for living systems.  This higher-order break in orthograde symmetry is a defining characteristic of an emergent dynamical transition. 

Deacon explains that living systems incorporate morphodynamic processes at nearly every level of their organization, from complex cycles of catalytic, an infrastructure amplifier.   molecular reactions to the embryonic cellular interactions which determine the elaborate theme-and-variation organization of plant and animal body architecture.  But he says organisms as whole dynamical systems, evolving lineages or embedded within ecosystems exhibit properties that differ radically from those characterizing morphodynamic processes:
  1. Organisms depend on and utilize energetic and material gradients to perform work to sustain constraints on their persistent, far from equilibrium dynamics.  
  2. Organisms actively reorganize their internal dynamics and relationships with the environment to counter or compensate for any depletion of necessary gradients. 
  3. Many organisms have evolved means of gradient assessment and spatial mobility that enable them to anticipate and avoid conditions of depleted gradients. 
  4. Organisms and ecosystems evolve toward forms of organization that increase the indirectness of the 'dissipation-path-length' of energy and material throughput in order to extract more work from the available gradients. 
Deacon concludes the ways that these processes all serve to maintain the capacity for self-repair and self-replication exemplify a clear inversion of the typical features of morphodynamic systems.  So an additional inflection separates living processes from morphodynamic processes.  This higher order dynamical form of organization promotes its own persistence and maintenance by modifying these dynamics to more effectively utilize supportive extrinsic conditions.  Deacon identifies an open orthograde recursive self-reconstitution and reproduction of the systems of constraint. 

Deacon argues organisms and the evolutionary process are not separable.  Explaining life requires explaining its evolutionary predisposition, because it must have emerged coextensive with whatever form of molecular teleodynamic process characterized the dawn of life.  Deacon focuses on accounting for the phase change in dynamical organization that necessarily occurred with the origins of life, irrespective of any specific molecular details.  Living and mental processes orthograde tendencies are triply complicated compared to the orthograde asymmetry of thermodynamic processes.   This is what provides their final causal character.  To resist the spontaneous degrading of thermodynamics requires work.  The maintenance of non-equilibrium conditions is essential, both for stabilization and for the generation of replacement components.  The work required is not merely energetic.  The incessant need to replace and reconstruct organism components depends upon synthetic form-generating processes, not merely resistance to breakdown. 

For Deacon reproduction is the construction of a dynamical physical system which is a replica of the system that constructed it, in both its structural and functional respects, though not necessarily a faithful replica in every detail.  Self-reproduction is thus an end-directed dynamic in which the end is only a potential general form represented within the dynamical system that produced it, but which is a physical system with the same general properties of its progenitor. 

Finally Deacon reviews Schrodinger's dual characterization of life as a marriage between transmission of information and non-equilibrium thermodynamics, the informational functions of life are emergent from and dependent on more basic non-equilibrium dynamical processes.  Generalizing the notions of metabolism supports the conversion of complex bonded structures present in food stuffs into simpler molecular structures and high energy molecules which can later be used to supply the energy needed to build complex bonded structures.  Nucleotide bases such as Adenosine (A) are used by biological cells as high energy 'intermediate' molecules.  Metabolism emerged in prokaryotic cells and in eukaryotic cells mitochondria provide this function. 
and containment, respectively, these processes can be described in terms of their roles in countering two thermodynamic challenges:
  1. There must be a mechanism that counters the incessant tendency for component elements of the system to degrade--either by repairing damaged components or by synthesizing new ones. 
  2. There must be a mechanism that resists the degradation of constraints on potential interactional relationships among components, such that the critical synthetic processes are reliably achieved. 
Deacon argues that this approach (autogenesis) is compatible with explaining the origin of teleodynamics since both approaches assume that the informational functions of life emerge from simpler dynamical foundations. 

Autogenesis

Deacon comments the logic of evolution must have emerged in the transition to ententional phenomena (teleodynamic processes).  Ententional properties like function and information will only be explained when we can demonstrate how they emerge from non-ententional precursors (thermodynamic/morphodynamic) through autocatalysis and self-assembly.  Deacon proceeds to do this. 

Autocatalysis
A cooperative set of catalysts, an infrastructure amplifier.   for a series of reactions results in autocatalysis.  Deacon comments that there are many analogs of autocatalysis in living cells.  It can arise spontaneously as a transiently locally deviant, non-equilibrium process.   But it requires a remarkably coincidental coalescence of reciprocally interlocking molecules, multiple atoms bonded together.  The physical and chemical phenomena associated with the molecule such as charge, size, shape, and potential energy reflect the constituent atoms, the types of bonds between them and the topology of the bonding.  Charged molecules dissolve in aqueous solutions (water).  Uncharged molecules dissolve in lipid bilayers.  , which is rare and seems on first thought improbable.  But Stuart Kauffman disagrees - he thinks in a polymeric soup many of the precursors will be somewhat catalytic.  Increasing the network connectivity will increase the catalysis of this set.  Then catalysis increases the key nodes and their products increasing the homogeneity of the reaction set.  Still eventually the success of the process will make the soup more homogeneous first amplifying and subsequently undermining the basis of the catalysis. 

Containment and self-assembly
Self-containment is a ubiquitous feature of life because life depends on the structural contiguity of its molecular systems remaining intact and unchanging.  The cell membrane, formed from a lipid (fat) bilayer which creates a barrier between aqueous (water soluble) media.  In AWF a key property of membranes - their providing a catalytic environment and supporting the suspension of enzymatically active proteins within the membrane; is simulated with a Workspace list where 'active' structures can be inserted and codelets can detect and act on the structure's active promise configured as an association in the Slipnet.   is a boundary distinguishing a continuously maintained self-similar milieu inside from a varying and unconstrained outside.  The finiteness of contained materials also makes the state space of their interrelationships manageable.  But a closed thermodynamic system quickly and inevitably runs down to a maximum entropy state.  Deacon consequently is interested in partial or periodic containment. 

Containment of
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organisms
and viruses is a relatively small capsule containing genetic material which utilizes the cellular infrastructure of its target host to replicate its genetic material and operational proteins.  The relationship with the host is short term, relative to parasites, with the virus entering the host cell, leveraging the host infrastructure to replicate its self massively and then exiting the host cell by rupturing it. 
is generally achieved by a ubiquitous molecular process of self-assembly.  The growth of multi-unit macromolecular structures is an expression of the intrinsic geometry of component molecules, the collective symmetries these offer in aggregate, and the lower energy state of the resulting form.  It is in this sense an expression of a thermodynamic orthograde tendency to reduce total entropy.  The influence of their structural and charge characteristics may contribute to the amplification of constraints, thereby generating regularities in the ways they form aggregates; a morphodynamic consequence. 

Synergy
Autocatalysis and self-assembly are self-limiting.  But the limitations are a source of synergy.  Together the two properties are reciprocally supportive. 

Self-assembly provides the conditions that are most critical for sustaining autocatalysis: the proximity of reciprocally interdependent catalysts. 

Reciprocally autocatalysis complements self-assembly.  The major consequence of autocatalysis is the continual production of identical molecules in the same region, whereas self-assembly is most robust if the concentration of component molecules is maintained despite depletion due to this process. 

Autogens
Deacon concludes the complementarity of the morphodynamic processes of self-assembly and auto-catalysis produces a special kind of emergent stability, unavailable to either process alone.  The reciprocal complementarity of these two self-organizing processes creates the potential for self-repair, self-reconstitution, and even self-replication in a minimal form. 

An autogen is an empirical type determined only by the continuity of those dynamic constraints which are themselves expressions of dynamical limitations - potential modes of change not expressed. 

Autogenic organization only exists with respect to a relevant supportive environment.  So autogenic individuation is also only defined with respect to a particular type of environment. 

The character of autogenic systems is a functional property. 

Autogenic evolution
Requirements for autogenic natural selection:
  1. Sufficient substrates to enable catalysis, but not so much as to disperse the catalytic set. 
  2. Competition among the autogenic lineages
  3. Variation among lineages
The self-reconstitutive dynamical synergy is the essential ingredient that precedes and underlies life.  This suggests that natural selection is ultimately an operation that differentially preserves certain alternative forms of morphodynamic processes compared to others, with respect to their synergy with one another, and with respect to the boundary conditions that enable them.  Selection is not then fully defined only with respect to replication of genetic information.  A self-maintaining formative power is critical.  This requires processes that generate, preserve and propagate constraints.  Morphodynamic processes are the only spontaneous processes that generate and propagate constraints, and autogens demonstrate that reciprocity between morphodynamic processes can preserve and replicate constraints. 

The ratchet of life
Autogens are not alive.  They are missing the ability to actively accumulate and mobilize energy within themselves.  But Deacon argues they do support a higher level ratchet effect which limits the increase in entropy.  Teleodynamic processes are constituted by the interactions between morphodynamic processes.  But the entropy flow maximization of these component processes is not additive in this interaction.  This is because the attractor basins toward which morphodynamic processes tend are specifically structured, and thus constitute constraints in their own right.  The complementary constraints that each generates with respect to the other are self-undermining.  Their progression toward optimal entropy production rate is also to a state where dynamical change ceases.  Regularity is built up, only to be frozen by closure.  Full dissipation is prevented at a point where optimal conditions for rapidly reinitiating the process are achieved.  An autogen is a negative entropy ratchet. 

The emergence of teleodynamics
Autogens mark the transition from maximum entropy production to constraint production and preservation, and from orthograde processes characterized by self-simplification to orthograde processes exemplified by self-preservation teleodynamics.  It's an emergent transition in the sense that the new orthograde organization is contrary to what proceeded. 

Deacon highlights the emergence of function.  The autocatalysis, the container, and the relationship between them are generated in each replication precisely because they are of benefit to an individual autogen's integrity and its capacity to aid the continuation of this form of autonomous individual.  It is the teleodynamic organization that causes this, and not merely some collection of interacting molecules, multiple atoms bonded together.  The physical and chemical phenomena associated with the molecule such as charge, size, shape, and potential energy reflect the constituent atoms, the types of bonds between them and the topology of the bonding.  Charged molecules dissolve in aqueous solutions (water).  Uncharged molecules dissolve in lipid bilayers.  , since these are replaceable.  Each component autogenic process is there for the sake of the autogen integrity.  Different features of the surrounding molecular environment contribute.  These are not glosses provided by a human observer, but intrinsic and functionally relevant features of the consequence-organized nature of the autogen itself. 

Deacon uses the identification of common logic in the hierarchy of emergent transitions to define emergence: An emergent dynamical transition is signaled by a change in the topology of the phase space of probable dynamic trajectories.  He writes 'Emergence is, in effect, defined by a polarity reversal in orthograde dynamics with ascent in scale'. 

Autogen dynamics demonstrates that there must be a morphodynamic intermediate between thermodynamics and living system dynamics. 

Ground work for an expanded science
Deacon applies his framework to various aspects of the world: work, information, significance, evolution, self, sentience and consciousness
Deacon's expanded conception of work
Contragrade change requires work utilizing a potential difference in entropy.  Deacon argues that how much things change from what would have otherwise occurred spontaneously is a reflection of the amount of work exerted to produce this change.  So long as contragrade change persists, work is involved, and thus it can accumulate over time and distance. 

Deacon argues that the generation of higher-order emergent dynamics depends on work at a lower order.  To understand the emergence of novel forms of causality, Deacon's argues you must explain the emergence and nature of higher-order forms of work. 

Deacon explores the nature of work broadly seeing it stretching into the realm of information.  Deacon views energy and information as analogous leveraging Gregory Bateson's ideas regarding Shannon, Claude Shannon was a key figure in information theory and computation.  He developed an electronic circuit using Boolean algebra which simplified the design and operation of a digital computer system enabling architectures such as Von Neumann's to become practical.  He also developed the mathematical models of information transfer which support information entropy. 
's theory of communication, which interpret information as a measure of variety or difference.  Information is not an actual thing.  Deacon suggests the generation of information might also be understood as a form of work.  While energy was initially viewed as a substance such ideas have been abandoned being replaced by a dynamic relational conception.  Work involves something that doesn't tend to happen spontaneously being induced to happen by something else that is happening spontaneously. 

Deacon argues that all forms of work as activity needed to overcome resistance to change.  Work can be seen as resulting from an orthograde process difference which creates the focus of a contragrade process which does work.  Macroscopic (orthograde) work depends on microscopic (thermodynamic) work being distributed in a very asymmetric way throughout the system. 

Deacon identifies a general principle of causality that shows how work and the constraints that make it possible are to be understood in terms of levels of scale and supervenient organization.  He continues framing a theory of morphodynamic work and of teleodynamic work.  Teleodynamic work is dependent on morphodynamic work is dependent on thermodynamic work.  In any context, orthograde processes will continue until they reach a state in which there is symmetry in the probable directions of change, or until the supportive conditions change.  This dynamical terminus of an orthograde process is its attractor, which may or may not be a quiescent state. 

Morphodynamic work
Morphodynamic orthograde processes are dynamically supervenient on incessant lower-order stable contragrade dynamics: the balance (symmetry) between incessant extrinsically introduced forms of destabilization, which introduce constraints, and the incessant spontaneous (orthograde) dissipation of these constraints.  Asymmetry arises under these conditions as constraints compound non-linearly.  As long as new extrinsic constraint is introduced faster than it is dissipated subsequent stages of change will exhibit progressively reduced ranges of variation. 

Teleodynamic work
Teleodynamic orthograde processes are more complex because they supervene on morphodynamic processes.  Teleodynamic patterns of change emerge from the contragrade interactions between morphodynamic processes.  Autocatalysis does thermodynamic work by asymmetrically increasing the local concentration of substrates for self-assembly, and self-assembly does thermodynamic work in impeding catalyst, an infrastructure amplifier.   diffusion.  In addition the interaction involves countervailing constraint generation processes, and thus morphodynamic work.  But morphodynamic regularities are rare under natural circumstances except in living systems.  The self-organizing processes impede the chaotic interactions which undermine other morphodynamic processes.   The process of biological evolution has discovered both how to setup a vast array of morphodynamic work processes and complex synergies and reciprocities between them that enable repeatable cycling.  Teleodynamic work is the production of contragrade teleodynamic processes. 

Deacon identifies what constitutes orthograde and contragrade processes in the teleodynamic domain of living
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organisms
:
  • Orthograde -
    • The actions of organisms that function to maintain them against degrading influences such as thermodynamic breakdown. 
    • Processes of growth, differentiation and reproduction which are involved in producing backup copies of the organism.  
  • Contragrade - teleodynamic processes that are organized so as to impede or contravene the orthograde processes. 
    • Deacon argues that these should be 'in some way' bad for the organism.  Reproductive competition from other members of the species is used as one example. 
Deacon argues that natural selection then allows teleodynamic work to transform one form of teleodynamic process into another, and to generate emergent phenomena at a higher level.  He argues that work done to acquire resources, mates, and so on is also work that degrades the teleodynamic efficacy of competitors with respect to these same arrangements.  This work is both directly and indirectly a source of distributed contragrade effects on other organisms. 

Deacon concludes the power to affect change at all levels is interconnected and interdependent.  Although the fundamental constants and laws of physics do not change, and there is no gain or loss of mass-energy during any physical transformation process, there can be quite significant alterations in the organizational nature of causal process.  Work can restructure the constraints acting as boundary conditions that determine what patterns of change will be orthograde in some other linked system.  The universe is open to organizational constraints on formal cause and the introduction of novel forms of efficient cause.  New forms of work can and are constantly emerging.  There is no limit to higher order forms of teleodynamic processes.  Thus the possibility of generating increasingly diverse forms of non-spontaneous dynamics can produce causal relationships that radically diverge from simple physical and chemical expectations, and yet still have these processes as their ground.  This is the essence of emergence, and the creative explosion it unleashes. 

Deacon's expanded conception of information
Shannon, Claude Shannon was a key figure in information theory and computation.  He developed an electronic circuit using Boolean algebra which simplified the design and operation of a digital computer system enabling architectures such as Von Neumann's to become practical.  He also developed the mathematical models of information transfer which support information entropy. 
's entropy and information model ignores reference. 

Deacon focuses on omissions, expectations and absences.  Regularities (expression of a constraint) allow omissions to become significant.  Hence Deacon concludes information is a feature of teleodynamic work.  Specific details of a sign's embodiment can be largely irrelevant.  Change of state requires a model that interprets it. 

Two entropies
Deacon introduces Boltzmann entropy, the association of thermodynamic entropy with increasing disorder and Shannon, Claude Shannon was a key figure in information theory and computation.  He developed an electronic circuit using Boolean algebra which simplified the design and operation of a digital computer system enabling architectures such as Von Neumann's to become practical.  He also developed the mathematical models of information transfer which support information entropy. 
entropy a measure of how much information a medium can possibly carry.  He notes that Boltzmann's conception is a dynamic property while Shannon's is structural.  Deacon goes on to explore dynamic properties of information.  He argues that work and selection can both be applied to signal dynamics.  He notes that reduced uncertainty is when a factor is hard to measure because it is dependent on many interconnected agents and may be affected by infrastructure and evolved amplifiers.  This is different from Risk.   equates to information - in the form of a referential sign about the nature of the work done in filtering the signal.  Reference implies that the receiver has some redundancy with what is already known (context) about the information conveyed by the signal. 

Deacon argues that though the external factors that alter a system's entropy are not intrinsic features of the medium, the signal constraint is an intrinsic feature.  Referential information is in this sense inferred from the form of the constraints embodied in the relationship between unconstrained possibility and the received signal.  In this way, Shannon information, assessed in term of this constraint, embodies a trace of the work that produced it.  Shannon information and referential information are not the same because the constraint is both intrinsic and yet not located in the signal medium.  Its a relationship between what  is and what could be. 

Deacon suggests the capacity to reflect the effect of work is the basis of reference.  In the case of classic information theory, the improbability of receiving a given sign or signal with respect to the background expectation of its receipt compared to other options defines the measure of potential information.  In the case of classic thermodynamics, the improbability of being in some far-from-equilibrium state is a measure of its potential to do work, and also a measure of work that was necessarily performed to shift it into this state.  The linkage between the two theories hinges on the materiality of communication (e.g. the constitution of its sign and/or signal medium).  So in a paradoxical sense, the absent content that is the hallmark of information is a function of the necessary physicality of the information process. 

Deacon's conception of significance
Interaction is required for a physical difference to become information.  Interpretation requires special forms of physical process to be produced.  It organizes work in response to the state of a sign medium and with respect to some normative consequence (valued over others). 

Information describes physical changes that get propagated from component to component in a designed or evolved feedback circuit only because the resultant attractor dynamics itself played the determinate role in generating the architecture of this mechanism. 

Deacon argues the capacity for one form of work to produce the constraints that organize another, independent form of work is the source of the amplifying power of information.  It provides the means for using the presence of a small energy gradient to create constraints that are able to organize the depletion of a much larger energy gradient.  Information can serve as the bridge linking the properties of otherwise quite separate and unrelated material and energetic systems.  Information expands the dimensions of Kauffman's adjacent possible in almost unlimited ways. 

What determines that a given constraint is information is that the interpretive process is organized so that this constraint is correlated with the generation of work that would preserve the possibility of this process recurring under some (usually most) of the conditions that could have produced this constraint.  The interpretive capacity is to generate a specific form of work in response to particular forms of system extrinsic constraints so that it generates intrinsic constraints that are likely to maintain or improve this capacity.  Only morphodynamic processes spontaneously generate intrinsic constraints.  Teleodynamics is needed to maintain the far from equilibrium conditions that maintain the morphodynamic processes. 

Interpretation
With the inclusion of reference a potentially infinite term is included in the quantification of information.  There must be interpretation to decide when the reference is fully resolved.  Interpretation must pick one factor in the trail of causes and effects leading up to the constraint reflected in the signal medium.  In different contexts and for different interpreters, the same sign or signal may thus be taken to be about very different things.  Resolution depends on the interpreting system, its intrinsic information-carrying /producing capacity and its involvement in the same causal chain. 

The causal history contributing to the constraints imposed on a given medium limits, but does not specify, what its information can be about.   That point in this causal chain that is the referent must be determined by and with respect to another information process.  All that is guaranteed by a potential reduction in Shannon, Claude Shannon was a key figure in information theory and computation.  He developed an electronic circuit using Boolean algebra which simplified the design and operation of a digital computer system enabling architectures such as Von Neumann's to become practical.  He also developed the mathematical models of information transfer which support information entropy. 
entropy of a signal is a possible linkage to something else.  This is an open-ended set of possibilities, only limited by processes that spontaneously obliterate certain physical traces or that block certain physical influences. 

An expansion of analytic tools effectively increases the Shannon entropy of a given physical trace - the interpretive process identifies a limited set of interpretable states from the total set.  Hence the interpretive process is also a signal producing process with its own potential Shannon entropy.  The maximum information that can be conveyed is the lesser of the Shannon entropies of the two processes. 

Noise versus error
Information can be in error but this can be mitigated:

Darwinian information
Evolution can be seen to use these error mitigation correspondences to generate information.  Noise becomes an additional signal:

Information emerging
Deacon sees three nested conceptions of information.  Shannon, Claude Shannon was a key figure in information theory and computation.  He developed an electronic circuit using Boolean algebra which simplified the design and operation of a digital computer system enabling architectures such as Von Neumann's to become practical.  He also developed the mathematical models of information transfer which support information entropy. 
information is the most minimal and basic.  Referential information (Boltzmann) is emergent from Shannon information, and significant--or useful--information (Darwinian) is emergent from referential information. 

Deacon concludes the ability to use extrinsically generated events and objects as information derives from the special dynamics of living processes.  The maintenance of intrinsically unstable, far-from-equilibrium conditions entails mechanisms that effectively anticipate the possible variations of environmental conditions by not excluding them. 

Representation
He continues constraints don't do work, but they are the scaffolding upon which the capacity to do work depends.  Even simple functional and representational relationships emerge from a nested interdependence of generative processes with constrained dynamics.  At the intersection of thermodynamics, natural selection and information theory entropy reduction and constraint generation allow the emergence of representation, reference and normativity (usefulness). 

Deacon's conception of evolution
Deacon argues that an adequate theory of evolution must include self-organization and selection.  Deacon comments that Darwin's theory of natural selection leaves out nearly all mechanistic details.  The ends justify the means by preserving them retrospectively.  True functional generality emerges from the process.  An adaptation is the realization of a set of constraints on candidate mechanisms, and so long as these constraints are maintained, other features are arbitrary.  Transmission of conserved constraints is critical (not energy, material or behavior).  In excluding the least helpful evolution creates a critical break in causal synergy that makes the concept of biological function an emergent general physical property. 

Still, Deacon comments, evolution must overcome the:
  • Degeneration of material by the second law of thermodynamics
  • Absence of a mechanism for generation, preservation and transmission of biological information. 
  • Requirement for a set of emergent teleodynamic systems to support the evolutionary process. 
He concludes that these are present in abiogenesis.  He uses  autogenic theory to act as a bridge from non-living to living processes.  It shows why spontaneous generation is so exceedingly rare.  Conditions that make it possible are highly precise and atypical of thermodynamically driven processes that are all but ubiquitous excepting life. 

Genetic information
Genetic information provides separately sequestered constraints embodied in some non-dynamic attribute, which can be preserved unmodified across changes in dynamics, so that earlier dynamical achievements will not be continually undermined.  It sequesters an independent source of constraint that is partially redundant to that intrinsic to the dynamics of the
This page reviews the implications of reproduction initially generating a single child cell.  The mechanism and resulting strategic options are discussed. 
organism
itself (Conserves and innovates).  In Deacon's earlier analysis of information it is associated with the transmission of constraints, exemplified by some physical medium linking a teleodynamic system with its environment.  Deacon argues it is therefore a derived feature of life.  This he concludes undermines Dawkin's Replicator approach.  He views the DNA (DNA), a polymer composed of a chain of deoxy ribose sugars with purine or pyrimidine side chains.  DNA naturally forms into helical pairs with the side chains stacked in the center of the helix.  It is a natural form of schematic string.  The purines and pyrimidines couple so that AT and GC pairs make up the stackable items.  A code of triplets of base pairs (enabling 64 separate items to be named) has evolved which now redundantly represents each of the 20 amino-acids that are deployed into proteins, along with triplets representing the termination sequence.  Chemical modifications and histone binding (chromatin) allow cells to represent state directly on the DNA schema.  To cope with inconsistencies in the cell wide state second messenger and evolved amplification strategies are used. 
sequence as analogous to Shannon information only. 

With an alternative autogenic interpretation Deacon explores a scenario where the semiotic status of autogens is extended with bonding, there are different types of chemical bonds.  Ionic bonds stabilize two oppositely charged ionized atoms when the negative atom gives up an electron to the positively charged atom.  Covalent bonds stabilize the two reactants when they adopt a more stable structure with electrons shared between them.  Hydrogen bonds stabilize charged groups when they are surrounded by water molecules.  In Copycat codelets can bond two Workspace objects together.  In the Smiley implementation a bondbuilder adds a bonding descriptor to one of the objects bonding it to the other. 
of relevant substrate molecules, multiple atoms bonded together.  The physical and chemical phenomena associated with the molecule such as charge, size, shape, and potential energy reflect the constituent atoms, the types of bonds between them and the topology of the bonding.  Charged molecules dissolve in aqueous solutions (water).  Uncharged molecules dissolve in lipid bilayers.   from the local environment to the autogens surface.  Deacon argues that if this increases the frequency of containment it also implies selective response to its environment (an adaptation in evolutionary biology is a trait that increased the number of surviving offspring in an organism's ancestral lineage.  In Deacon's conception of evolution an adaptation is the realization of a set of constraints on candidate mechanisms, and so long as these constraints are maintained, other features are arbitrary. 
).  Binding of substrate becomes information about the suitability of the environment for successful replication.  Deacon concludes that this information is specifically about the environment for the maintenance of this interpretive capacity

Deacon goes on to extend the scenario to generate an additional level of referential information.  He argues that if the binding substrate is a nucleotide its monomeric features (energy transfer and signalling) once leveraged by the autogen allow the later emergence of the information conveying capability.  He argues that autogen catalysis and/or self-assembly is potentiated by the bound nucleotide.  Subsequently during the reconstitution/replication phase of the autogen energy from the nucleotides is used as fuel.  Such augmented autogen systems would have an evolutionary advantage through energy leverage.  Significantly the autogen's inherent constraints would then be beneficially affected by the sequestering of 'spare' nucleotide in a compacted separated but internal phase allowing the autogen to conclude its general cycle. 

Deacon argues that the sequestration of nucleotide independently enables the additional functions based on sequence when these support needed constraint creation/preservation/replication.  Deacon concludes morphology reproducing autogens with energy cycling can enable the emergence of information replicating semeota. 

Deacon's conception of Self
Deacon's central thesis is that the core property of self is a special form of dynamical organization: teleodynamics.  All teleodynamic processes are implicitly individuated.  They are closed with respect to other dynamical features of the world.  Each component function contributes to the continued existence of the whole and the whole is required to generate each component function. 

Deacon comments that the source of agency can be described as the generation of interactive constructions which do work to perpetuate the reciprocal maintenance of the constraints that maintain the organism. 

Deacon sees evolution as freeing agents from nominalism.  Physical responses, perceptions and mental categories aren't merely passive reflections on the world; they exist to structure adaptation in evolutionary biology is a trait that increased the number of surviving offspring in an organism's ancestral lineage.  In Deacon's conception of evolution an adaptation is the realization of a set of constraints on candidate mechanisms, and so long as these constraints are maintained, other features are arbitrary. 
to the world.  For this reason Deacon argues the mere resemblance of an object to a perceptual class can be what causes the object to be modified in a particular way by an animal or person.  This augmented efficacy of generals is a feature that emerges from teleodynamics.  It is an attribute of life itself.  Individuation and agency are intrinsic features of teleodynamics which brains have evolved to generate, because of the dynamical closure, constraint generation, and self-maintenance that defines teleodynamics.  Deacon argues that the brains 'self' has a higher order teleodynamics since it must model itself.  As such the self is embodied by dynamical constraints. 

Deacon's conception of sentience
Deacon follows William James's view of the background 'feeling of being here' which is seen as a distinctive quality of experience that is private, internal and self-referential and with which the non-self content is discriminated, as being sentience. 

Because organisms are teleodynamic systems, they do not merely react mechanically and thermodynamically to perturbation, but generally are organized to initiate a change in their internal dynamics to actively compensate for extrinsic modifications or internal deficits.  Feeling is in this basic sense active. 

Deacon asserts that complex intentional features that characterize our thoughts and objective experiences emerge from a background of neurological morphodynamic and homeodynamic processes.  Moreover, these lower-order subvenient dynamical features must also inevitably constitute significant aspects of our mental lives.  Deacon believes that once a mechanistic and computational framework for intentional content is abandoned its characterization will be open to empirical analysis linking cellular-molecular processes to intentional features of mental experience. 

As with Deacon's analysis of emergent constraints on evolution he sees the brain's mechanistic properties as being necessarily constrained by emergent requirements. 

The relevant interpretive process must be intrinsic.  Deacon assumes that neurons, specialized eukaryotic cells include channels which control flows of sodium and potassium ions across the massively extended cell membrane supporting an electro-chemical wave which is then converted into an outgoing chemical signal transmission from synapses which target nearby neuron or muscle cell receptors.  Neurons are supported by glial cells.  Neurons include a:
  • Receptive element - dendrites
  • Transmitting element - axon and synaptic terminals
  • Highly variable DNA schema using transposons. 
have been adapted, over the course of evolution, to use some of their otherwise generic metabolic and intercellular communication capabilities for the special purpose of conveying point-to-point signals between one another.  The mechanisms are unruly, noisy and only modestly reliable transducers and conveyers of signals.  Neurons still have to perform a great many non-signal transmission tasks that are necessary for any call to stay alive. 

Deacon adds that most brains, from simple to large and complex appear to be deployed based on a broadly similar amount of genetic material.  Replication of architecture appears to allow for increases in size and complexity, M. Mitchell Waldrop describes a vision of complexity via:
  • Rich interactions that allow a system to undergo spontaneous self-organization
  • Systems that are adaptive
  • More predictability than chaotic systems by bringing order and chaos into
  • Balance at the edge of chaos 
.  Hence Deacon argues brains are not well suited to be digital computing systems, which require predictability, and reliability.  Instead mammalian brains are astronomically huge, highly interconnected, highly reentrant networks, where noise is likely to get wildly amplified. 

Deacon suggests instead noise must be a design feature of brains, rather than something to be eliminated.  Deacon sees the network of neurons as supporting emergent dynamic processes.  Deacon suggests whole brain sentience is a function of dynamical regularities at a more global level than signals within individual nerve cells, which equate more to the homeodynamic  flow's individual components discussed earlier. 

Deacon suggests that brains specifically evolved in animate multicelled creatures because being able to move about and modify the surroundings require predictive as well as reactive capabilities.  He argues that the evolution of this 'anticipatory sentience' -- nested within, constituted by, and acting on behalf of the 'reactive sentience of the organism -- has given rise to emergent features that have no precedent. 

As with his analysis of evolution Deacon extends the autogen.  This time to support a minimal sentience.  He proceeds to use this approach to explore the implications for
John Searle's influential thought experiment implied to him that computers cannot understand.  Complex adaptive system (CAS) theory indicates that this is not the case. 
Searle's Chinese Room
.  Deacon concludes Searle intends to illuminate the difference between a mechanistic (homeodynamic) process and an ententional (teleodynamic) process.  The Chinese room can be augmented to precisely identify what is missing which should be a metric for determining whether a given brain process is merely computational or is also sentient.  Just as it was necessary to stop trying to identify the teleodynamics of life with molecular dynamics alone but instead one had to attend to the constraints embodied as well, computational mechanics alone cannot be viewed as mapping to intentional properties of mentality. 

Deacon argues that first it is necessary to understand the teleodynamic features that emerge in a tangled hierarchy within nervous systems.  Deacon describes starting this process in his final chapter on consciousness

Deacon's conception of consciousness
Deacon views consciousness as a second order emergent sentience - a sentience of sentience.  As such it is able to constrain, detect and alter the first order emergent functions of sentience.  What results is a sentience of the normative features of sentience: pleasure, pain amplifies the aggression response of people by interoceptive signalling of brain regions providing social emotions including the PAG projecting to the amygdala; making aggressive people more so and less aggressive people less so.  Pain is the main reason people visit the ED in the US.  , joy and suffering. 

Deacon argues that any teleodynamic system generates an emergent sentience.  Higher animals develop a multi-layer ententional hierarchy.  He sees neuron networks, a network of interconnected neurons which perform signalling, modeling and control functions.  In Cajal's basic neural circuits the signalling is unidirectional.  He identified three classes of neurons in the circuits:
  • Sensory, Interneurons, Motor; which are biochemically distinct and suffer different disease states. 
as providing a low level teleodynamic substrate.  It is based on morphodynamics and thermodynamics.  Deacon presents the flows of blood to the neurons, specialized eukaryotic cells include channels which control flows of sodium and potassium ions across the massively extended cell membrane supporting an electro-chemical wave which is then converted into an outgoing chemical signal transmission from synapses which target nearby neuron or muscle cell receptors.  Neurons are supported by glial cells.  Neurons include a:
  • Receptive element - dendrites
  • Transmitting element - axon and synaptic terminals
  • Highly variable DNA schema using transposons. 
, and control of these as essential thermodynamic characteristics and constraints.  Attractors emerging from these teleodynamic and morphodynamic flows support higher level morphodynamics and teleodynamics. 

Deacon writes 'There are emergent sentient properties produced by the teleodynamics of brains that are not produced by simpler, lower-order forms of sentience.  Crucially, these are special normative properties made possible because the sentience generated by brain processes is, in effect, a second-order sentience.'  He further explores the implications of having a teleodynamic process include within itself a representation of its own dynamical final cause tendencies.  'For animals with brains, the organism and its distinctive teleodynamic characteristics will likely fail to persist (both in terms of resisting death and reproducing) if its higher-order teleodynamics of self-prediction fails in some respect.' 

He concludes 'Generation of a projected future self-in-context thus can become a critical source of constraints organizing the whole system.  But generating these virtual selves requires both a means to model the causality of the environment and also a means for modeling the causality of the teleodynamic processes that generate these models and act with respect to them.'  ... 'In an animal with a brain that was evolved to project alternative future selves-in-context, such an assessment [of overall integrity] becomes a relevant factor.  A separate dynamical component of its teleodynamic organization must continually generate a model of both its overall vegetative integrity and the degree to which this is (or might be) compromised with respect to other contingent factors.  A dynamical sub process evolved to analyze whatever might impact persistence of the whole organism, and determine an appropriate organism level response, must play a primary role in structuring its overall teleodynamic organization.' 

Deacon argues pain is how neural teleodynamics reorganizes in response to its sensory assessment of vegetative damage.  Its effect is to interrupt less critical neural dynamics and activate specific processes to stop this sensory signal.  To do this it must block the differentiation of most morphodynamic processes that are inessential to this end, and rapidly recruit significant metabolic and neural resources to generate action to avoid continuation of this stimulus. 

Deacon views the expanded notion of science as enabling a fuller understanding of the architectures and operations of conscious brains.  He writes even though this is a theory which defends the thesis that intentional relationships and sentient experiences are not material phenomena in the usual sense of that concept, it nonetheless provides us with a thoroughly empirical set of predictions and testable hypotheses about these enigmatic relationships. 

Complex adaptive system
This page introduces the complex adaptive system (CAS) theory frame.  The theory is positioned relative to the natural sciences.  It catalogs the laws and strategies which underpin the operation of systems that are based on the interaction of emergent agents. 
John Holland's framework for representing complexity is outlined.  Links to other key aspects of CAS theory discussed at the site are presented. 
(CAS) theory
depends directly on the
Flows of different kinds are essential to the operation of complex adaptive systems (CAS). 
Example flows are outlined.  Constraints on flows support the emergence of the systems.  Examples of constraints are discussed. 
dynamic flows, constraints
, self-assembly and
This page discusses the mechanisms and effects of emergence underpinning any complex adaptive system (CAS).  Key research is reviewed. 
emergence
which Deacon explores. 

He demonstrates key relationships between interacting flows, constraints on these flows, and the emergence of higher level dynamic phenomena
This page reviews the implications of selection, variation and heredity in a complex adaptive system (CAS).  The mechanism and its emergence are discussed. 
Evolution
gains mechanistic support and remains essential to the development of CAS. 

Our conception of
Plans are interpreted and implemented by agents.  This page discusses the properties of agents in a complex adaptive system (CAS). 
It then presents examples of agents in different CAS.  The examples include a computer program where modeling and actions are performed by software agents.  These software agents are aggregates. 
The participation of agents in flows is introduced and some implications of this are outlined. 
agents
intrinsically bound to
Plans emerge in complex adaptive systems (CAS) to provide the instructions that agents use to perform actions.  The component architecture and structure of the plans is reviewed. 
schematic structures
while consistent with Deacon's theories places more significance on their impact on higher level emergent systems.  Deacon argues that genetic structures ensure successful dynamic systems persist across generationsWe similarly extend Blackmore's memetic model to include dependencies on the infrastructure that supports the flows, constraints and associative signaling that enables the emergence of memetic systems.  We view books, educational processes and neuronal long term memory in the brain includes functionally different types: Declarative (episodic and semantic), Implicit, Procedural, Spatial, Temporal, Verbal; Hebb noted that glutamate receptive neurons learn by (NMDA channel based) synaptic strengthening.  This strengthening is sustained by subsequent LTP.  The non-realtime learning and planning processes operate through consciousness using the working memory structures, and then via sleep, the salient ones are consolidated while the rest are destroyed and garbage collected.   structures as persisting valuable dynamic processes across generations of brains. 

Deacon's frustration with computer based 'evolutionary systems' failing to represent the essential physical constraints of the real world seems justified.  The failure distorts the representation of the environment and the pressures on the agents making it difficult to explore the adjacent possible.  AWF's agent programming framework
This page describes the Adaptive Web framework (AWF) test system and the agent programming framework (Smiley) that supports its operation. 
Example test system statements are included.  To begin a test a test statement is loaded into Smiley while Smiley executes on the Perl interpreter. 
Part of Smiley's Perl code focused on setting up the infrastructure is included bellow. 
The setup includes:
  • Loading the 'Meta file' specification,
  • Initializing the Slipnet, and Workspaces and loading them
  • So that the Coderack can be called. 
The Coderack, which is the focus of a separate page of the Perl frame then schedules and runs the codelets that are invoked by the test statement structures. 
Smiley
's chemical foundation, barriers to bonding, there are different types of chemical bonds.  Ionic bonds stabilize two oppositely charged ionized atoms when the negative atom gives up an electron to the positively charged atom.  Covalent bonds stabilize the two reactants when they adopt a more stable structure with electrons shared between them.  Hydrogen bonds stabilize charged groups when they are surrounded by water molecules.  In Copycat codelets can bond two Workspace objects together.  In the Smiley implementation a bondbuilder adds a bonding descriptor to one of the objects bonding it to the other. 
based on
This page describes the Copycat Slipnet. 
The goal of the Slipnet is reviewed. 
Smiley's specialized use of the Slipnet is introduced. 
The initial Slipnet network used by the 'Merge Streams' and 'Virtual Robot' agent-based applications is setup in initchemistry and is included. 
The Slipnet infrastructure and initialization functions are included. 
Slipnet
properties, salience, Douglas Hofstadter controlled the amount of attention a Workspace object in Copycat would receive from codelets via its salience.  The more descriptions, analogous to geons, an object has and the more highly activated the nodes involved therin, the more important the object is.  Modulating this tendency is any relative lack of connections from the object to the rest of the objects in the Workspace.  Salience is a dynamic number that takes into account both these factors.  In Smiley the instantaneous salience of a Workspace's objects is calculated by itsalience.   requirements of the
This page describes the Copycat Coderack. 
The details of the codelet architecture are described. 
The specialized use of the Coderack by the adaptive web framework's (AWF) Smiley is discussed. 
The codelet scheduling mechanism is discussed. 
A variety of Smiley extensions to the Coderack are reviewed. 
The Coderack infrastructure functions are included. 
Coderack
, the
This page discusses how Smiley provides deployment guarantees to its agent-based applications. 
Smiley's transaction services are reviewed. 
The complex interactions of codelets participating in a deployment cascade are discussed including: 
  • The implementation of schematic switches. 
  • The cooperative use of goal suppression.  
  • Evaluator codelets promotion of other siblings. 
Challenges of initiation of a cascade are discussed. 
Tools to associate transaction protection to an operon deployed codelet are described. 
Special support for sub-program codelets is described.  Completion of transactional sub-programs presents special challenges. 
Priority and synchronization support includes:
  • Delaying the operaton of the cascade sponsor. 
  • Delaying the notgcompleting cascade participant. 
  • Waiting for completion of parallel operations with the wait and relay service.  
The need to sustain resource pools is reviewed. 
The use of signals to coordinate siblings is described. 
The structural binding operon for the wait and relay service is included. 
The codelets and supporting functions are included.
cascading flows
of codelets and its consumption of free energy as the codelets operate starts to add back these constraints. 

Deacon's opus provides a vision of an expanded science that includes frameworks for emergent systems.  He demonstrates how dynamic processes can synergistically constrain entropy, self-assemble and auto catalyze inducing the emergent and evolutionary properties of real CAS systems.



































































  


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This page looks at schematic structures and their uses.  It discusses a number of examples:
  • Schematic ideas are recombined in creativity. 
  • Similarly designers take ideas and rules about materials and components and combine them. 
  • Schematic Recipes help to standardize operations. 
  • Modular components are combined into strategies for use in business plans and business models. 

As a working example it presents part of the contents and schematic details from the Adaptive Web Framework (AWF)'s operational plan. 

Finally it includes a section presenting our formal representation of schematic goals. 
Each goal has a series of associated complex adaptive system (CAS) strategy strings. 
These goals plus strings are detailed for various chess and business examples. 
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