Accumulating small changes
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Accumulating small changes

Summary
Richard Dawkin's explores how nature has created implementations of designs, without any need for planning or design, through the accumulation of small advantageous changes. 
The Blind Watchmaker
In Richard Dawkin's book 'The Blind Watchmaker' he explains that while the un-designed development of heterogeneous structures seems highly improbable there is a credible mechanism, which he describes.  At each stage in the accumulation of changes an
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. 
agent
must make a living for long enough to reproduce.  Dawkins views the agent structured as a reductionist hierarchy.  The accumulation is non-random, filtered by natural selection's killing non-viable changes.  Dawkins highlights the confusion of many who imagine that natural selection is random.  If this was true it would make the accumulation process collapse. 

Dawkins uses echo location in bats to demonstrate good solutions to the challenge of making a living in the dark. The solution can also be seen in use by whales, insects, fish, blind humans, and in designed human tools such as RADAR is radio detection and ranging.  It is a method of finding the position and velocity of a target by sending out a pulse of radio frequency electromagnetic waves and analyzing the reflections returned from the target.  .   Alternatives such as search lights were probably too energy intensive to compete in most niches. 

Dawkins catalogs aspects of the bat's solutions, such as beam ultrasound, Doppler Shift, pitch shift, signal echo match and filtering, and variable strobe which have also been necessary to make RADAR viable. 

To illustrate the consequences of accumulation of small changes Dawkins developed a small computer program which generates shapes, called biomorphs, displayed on a screen. The program consists of a:

Dawkins develops a picture of a biomorph mathematical space representing all possible biomorphs.  To transform directly from one biomorph to another would require a transformation of all the altered gene values, which is a statistical impossibility within the time from the big bang to now.  But with the accumulation of single value changes during each of the many generations one biomorph is seen to transform into another.  Dawkins mutational restriction, only a single change per reproduction, is justified by the need for each generation to remain viable at survival and reproduction.  Extensive changes are likely to be lethal, so natural selection will encourage small changes.  Indeed real animals have controls to limit the extent of discrete mutational changes. 

Dawkins introduces an analogous animal mathematical space.  He argues that an animal without an eye are major sensors in primates, based on opsins deployed in the retina & especially fovea, signalling the visual system: Superior colliculi, Thalamus (LGN), Primary visual cortex; and indirectly the amygdala.  They also signal [social] emotional state to other people.  And they have implicit censorious power with pictures of eyes encouraging people within their view to act more honorably.  Eyes are poor scanners and use a saccade to present detail slowly to the fovea.  The eye's optical structures and retina are supported by RPE.  Eyes do not connect to the brain through the brain stem and so still operate in locked-in syndrome.  Evo-devo shows eyes have deep homology.  High pressure within the eye can result in glaucoma.  Genetic inheritance can result in retinoblastoma.  Age is associated with AMD. 
can be transformed into one with an eye of apparently complex design, through accumulation of small changes that in aggregate express an eye.  The habitat of the animal encouraged the accumulation.  Dawkins notes that similar habitats have resulted in convergent evolution.  He views the continuous nature of the variables in habitats as supporting evolution.  Slight changes will result in slight improvements, and such changes will correspond to a competitive advantage.  Dawkins lists examples of such incremental advantages, as in wing development. 

However, Dawkins also highlights the constraint that incremental accumulation implies.  New features will develop by transforming current features, and not by starting afresh which he outlines using the development of flatfish.  Dawkins notes the difference with engineering approaches. 

Dawkins describes the properties of
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. 
genes
: information represented in a compressed medium, which can be replicated.  The information includes an addressing scheme.  A species can be defined by its sharing the same addressing scheme.  The information is transcribed is the process where DNA is converted into messenger m-RNA.  A complex of enzymes cooperates to bind to the DNA and generate the m-RNA copy.  There are a number of such transcription complexes which are based on RNA polymerase I, II or III. 
and translated is the process where messenger m-RNA is cross coded by Ribosomal agents and t-RNA into an amino-acid polymer.   into phenotypic is the system that results from the controlled expression of the genes.  It is typically represented by a bacterial cell or the body of a multi-cell animal or plant.  The point is that the genes provide the control surface and the abstract recipe that has been used to generate the cell. 
effects which enable competitive advantage in surviving and reproductive selection.  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. 
is highly conserved through each replication event.  Dawkins sites histone, in the eukaryotic cell are enzymes which bind to the DNA polymers supporting them and controlling their interactions with other enzymes.  In particular sets of DNA operons can be enabled or disabled by histone induced changes in the DNA polymers shape.  In AWF the histone control of DNA has been abstracted in a codelet based implementation of operon controlled programmed case control. 
H4 which is conserved between peas and cows!  Natural selection is seen as a constraint on the natural mutation rate, which is already very low due to the presence of repair and proof reading mechanisms. 

Dawkins suggests the presence of three ingredients that ensure the accumulation of small changes:
  1. Self-replication - Dawkins explores alternatives to DNA more likely to have been part of the initiator event. 
  2. Copying errors
  3. Power over the future - having an influence over their probability of being replicated.  There are direct and indirect effects.  Eyes are major sensors in primates, based on opsins deployed in the retina & especially fovea, signalling the visual system: Superior colliculi, Thalamus (LGN), Primary visual cortex; and indirectly the amygdala.  They also signal [social] emotional state to other people.  And they have implicit censorious power with pictures of eyes encouraging people within their view to act more honorably.  Eyes are poor scanners and use a saccade to present detail slowly to the fovea.  The eye's optical structures and retina are supported by RPE.  Eyes do not connect to the brain through the brain stem and so still operate in locked-in syndrome.  Evo-devo shows eyes have deep homology.  High pressure within the eye can result in glaucoma.  Genetic inheritance can result in retinoblastoma.  Age is associated with AMD. 
    , eco-location etc. exert indirect effects on survival and replication of their DNA. 
Dawkins explains why the initial emergence of a self-replicating agent was exceptionally unlikely:
  • It's a highly improbable single event, since a compound event would have suffered from multiplied unlikelihood. 
  • But is helped by the existence of billions of planets, and huge amount of time since the big bang. 
Unfortunately, human judgment is selected for its application to our local environment, matched to the timescales of our lives of decades, experienced velocities, and statistically likely events.  We are ill equipped to make judgments about the initiator event. 

Genes are part of the environment of each other. 
  1. It is a team of genes that evolves. 
    This page reviews the inhibiting effect of the value delivery system on the expression of new phenotypic effects within an agent. 
    Extended phenotypic alignment
    will support the team's domination.  Existing phenotypic processes are affected by all the genes that contribute to the gene pool across time and space.  They can optimize the route taken to reduce competition in the phenotype.  With the development of multi-cellular eukaryotes, a relatively large multi-component cell type from which yeast and multi-celled plants and animals, including humans, is constructed.  It contains modules including a nucleus and production functions such as mitochondria.   'design' possibilities expanded. 
  2. Genes also influence each other's environments in competition, creating
    This page reviews the strategy of setting up an arms race.  At its core this strategy depends on being able to alter, or take advantage of an alteration in, the genome or equivalent.  The situation is illustrated with examples from biology, high tech and politics. 
    multi-competitor arms races
    , which are important, in contrast to natural selection, in positively enhancing the retention of beneficial mutations.  The environment is progressively changed, as
    This page introduces a series of asymmetries which encourage different strategic approaches.   
    The differences found in business, sexual selection, gamete structure, as well as in chess encourage escalations in the interactions. 
    And yet the systems including these asymmetries can be quite stable. 
    asymmetric changes
    by the competitors are built upon. 
Genetic competitions can induce positive returns, W Brian Arthur's conception of how high tech products have positive economic feedback as they deploy.  Classical products such as foods have negative returns to scale since they take increasing amounts of land, and distribution infrastructure to support getting them to market.  High tech products typically become easier to produce or gain from network effects of being connected together overcoming the negative effects of scale.  .  Dawkins highlights two significant examples:
With the accumulation of small changes 'gradualism' providing such a consistent explanation of evolved life, Dawkins expresses frustration at the advocates of macro mutations, and species selection.  Macro mutations were shown by Fisher to be risky.  Dawkins sees new species forming, and replacing prior species in the fossil record, due to the initial species
Barriers are particular types of constraints on flows.  They can enforce separation of a network of agents allowing evolution to build diversity.  Examples of different types of barriers and their effects are described. 
separating into two geographically isolated groups
.  Later if the two
This page reviews Christensen's disruption of a complex adaptive system (CAS).  The mechanism is discussed with examples from biology and business. 
reconnected, and the further evolved group out competed its ancestor species
an apparent gap would appear in the fossil record seen at the site. 

In the Blind Watchmaker Dawkins argues for one true tree of life, with perfect nesting.  This is based on the similarity of the DNA plan of all living things.  However, the way the branches are arranged, and where they started from, is still unknown.  For Dawkins the separation of two sets within the tree is just a formalism.  If enough of the ancestors were identified the separations would be seen to be arbitrary.  Some paleontologists disagree. 

Dawkins compares Darwinian selection (the accumulation of small changes) with Lamarckism, neutralism, mutationism, molecular drive, and creationism.  All the alternatives struggle to retain useful changes incrementally.  Lamarckism has to identify useful changes and retain only these, but how can they be identified, except by the filtering effect of natural selection?  Neutralism accepts natural selection is required 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. 
so it is moot for Dawkins focus in this book.  Mutationism has no mechanism to select beneficial changes.  It is argued that mutations are non-random and Dawkins accepts this is likely, but the non-random action must still be capable of creating eyes are major sensors in primates, based on opsins deployed in the retina & especially fovea, signalling the visual system: Superior colliculi, Thalamus (LGN), Primary visual cortex; and indirectly the amygdala.  They also signal [social] emotional state to other people.  And they have implicit censorious power with pictures of eyes encouraging people within their view to act more honorably.  Eyes are poor scanners and use a saccade to present detail slowly to the fovea.  The eye's optical structures and retina are supported by RPE.  Eyes do not connect to the brain through the brain stem and so still operate in locked-in syndrome.  Evo-devo shows eyes have deep homology.  High pressure within the eye can result in glaucoma.  Genetic inheritance can result in retinoblastoma.  Age is associated with AMD. 
and echo location which seems unlikely.  Molecular drive suggests that each incremental change is a random process, which only becomes beneficial when the change becomes matched with a new environment.  Dawkins considers the combinatorial explosion implied to make the theory untenable for developing eyes etc.  Finally Dawkins has no need of creationism since natural selection can provide an explanation without the need for further assistance. 

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
This page reviews the implications of selection, variation and heredity in a complex adaptive system (CAS).  The mechanism and its emergence are discussed. 
evolution


Dawkins argument that implementations of designs are reducible to physical principles disagrees with our understanding of
This page discusses the mechanisms and effects of emergence underpinning any complex adaptive system (CAS).  Key research is reviewed. 
emergence
as discussed in Incomplete Nature by Terrence Deacon and
Russ Abbott explores the impact on science of epiphenomena and the emergence of agents. 
Emergence Explained
by Russ Abbott

Dawkins says that apparent design and planning in natural systems are illusions.  However, natural selection is obviously capable of implementing mechanisms that can consequently plan and design.  The
Walter Shewhart's iterative development process is found in many complex adaptive systems (CAS).  The mechanism is reviewed and its value in coping with random events is explained. 
Shewhart cycle
is instantiated in the cell cycle, a key control mechanism in eukaryotic cells ensures that the cell can replicate when required.  The process is complicated but is logically equivalent to a Shewhart cycle with four phases: (1) general operation using the DNA as the plan, (2) generation of copies of genetic material, (3) checking that the copies were robust, (4) separation of the cell into two.  The details of the cell-cycle are described by Helmreich.  In AWF the eukaryotic cell-cycle has been abstracted in a codelet based implementation. 
, where DNA plans are deployed, checked, and corrected prior to cell division.  Further the emergence of an epiphenomenal goal 'deploy eye' associated with the addressable schemata that deploys an eye does not seem illusionary.  Indeed in different species the identical mechanism of signalling, is an emergent capability which is used by cooperating agents to support coordination & rival agents to support control and dominance.  In eukaryotic cells signalling is used extensively.  A signal interacts with the exposed region of a receptor molecule inducing it to change shape to an activated form.  Chains of enzymes interact with the activated receptor relaying, amplifying and responding to the signal to change the state of the cell.  Many of the signalling pathways pass through the nuclear membrane and interact with the DNA to change its state.  Enzymes sensitive to the changes induced in the DNA then start to operate generating actions including sending further signals.  Cell signalling is reviewed by Helmreich.  Signalling is a fundamental aspect of CAS theory and is discussed from the abstract CAS perspective in signals and sensors.  In AWF the eukaryotic signalling architecture has been abstracted in a codelet based implementation.  To be credible signals must be hard to fake.  To be effective they must be easily detected by the target recipient.  To be efficient they are low cost to produce and destroy. 
'deploy eye' results in the deployment of two radically different types of eye. 

Dawkins contrasting of evolved 'designs' and engineers design approach aligns with Arthur's description of the
Tools and the businesses that produce them have evolved dramatically.  W Brian Arthur shows how this occurred.
evolution of technology
.  Again we would argue that engineers are typically constrained to iteratively evolve their systems by the pressure of
This page reviews the inhibiting effect of the value delivery system on the expression of new phenotypic effects within an agent. 
extended alignment
.  

Dawkins discussion of genetic addressing schemes is formalized in CAS theory as the presence of associative structures in the schemata and other constructions built by agents which can consequently be operated on by the agents under schematic control. 

Dawkins argument for perfect nesting within the tree of life seems at odds with our understanding of the shared nature of schematic structures.  With virus 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. 
and plasmid provide bacteria with a way to transfer parts of their DNA complement with one another.  The effect is to ensure that useful mutations can become rapidly distributed within a population of bacteria.   vectors moving DNA between different hosts it is at best a blurred representation. 

The Blind Watchmaker clearly demonstrates how evolution, through the non-random accumulation of small advantageous changes, has no requirement for design or planning.  

























































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Each goal has a series of associated complex adaptive system (CAS) strategy strings. 
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