Intro to Complexity Science: Part 2: Emergence and Evolution - Constraints on Form

[Jonathan]

Emergence and Evolution - Constraints on Form
by Chris Lucas


"The view of evolution as chronic bloody competition among individuals
and species, a popular distortion of Darwin's notion of 'survival of the
fittest,' dissolves before a new view of continual cooperation, strong
interaction, and mutual dependence among life forms. Life did not take
over the globe by combat, but by networking."

Lynn Margulis and Dorian Sagan, Slanted Truths, 1997

"The emergent qualities that are expressed in biological form are
directly linked to the nature of organisms as integrated wholes; these
can be studied experimentally and simulated by the use of complex
non-linear models."

Brian Goodwin, How the Leopard Changed its Spots, 1994, Ch 7

Introduction

Organization is a common feature of the world around us, so it is
natural to consider how these structures arise. Since Darwin it has been
assumed that 'Natural Selection' is an adequate mechanism to explain all
the non-physics features of life. Yet this approach neglects both the
self-organizing aspects of physical systems and the goal driven
behaviour (teleology) of higher organisms.

Recent work on cellular structures shows that chemical systems often
organize themselves into complex forms, examples include viruses,
protein folding and microtubules. Form can thus be an integral aspect of
a system and not 'selected for' by external forces. Additionally,
organisms make choices, they do not behave passively under environmental
selection but act to change those forces. Taking account of these
influences leads us to take a rather more coevolutionary approach to
natural selection, incorporating insights from complex systems science.

Selective Forces

It is well known in physics that gravity and electromagnetic forces both
can act from outside a system (fields) and within (interconnections). To
some extent this is just a difference in our viewpoint, whether we
include the 'source' in our system or not - if the source is much larger
than the other components then it makes sense to treat it as an external
invariant, simplifying the equations (the effect of the 'system' on the
source is then considered negligible).

This thinking pervades evolution also, with the view that 'selection' is
an external force, a fixed 'fitness function' shaping the organism. In
some cases this seems to be a reasonable viewpoint, for example if a
predator (the external force) can more easily catch slow prey then there
will be survival advantages in evolving general speed, defence or
disguise adaptations. Yet even here it is clear that the actual
'adaptation' isn't a function of the selective force, that only has the
effect of choosing between the available options - in this case between
slow, fast, dangerous or disguised 'prey systems', which must each arise
via alternative methods. It should be noted that selection does not
select 'for' a characteristic, only 'against' a disadvantageous one, all
'successful' adaptations avoid selection; as do any good, bad or
indifferent changes that don't have 'selective' relevance to any
particular 'culling' process. What is passed on to the next generation
is the overall package, warts and all.

Model Simplifications

We need to be clear before discussing these issues just what
generalisations are being made. In many treatments, particularly in
Artificial Life, it is assumed that there are populations of organisms
with the same genotype, that the fitness measure applies equally to all
organisms regardless of environmental location, that it is constant with
time, that it is independent of other traits, that it is independent of
population size and so on. None of these simplifications will be true in
'real' systems, other than in restricted circumstances, so we must be
wary of excessive extrapolations of theoretical results.

Phenotypic properties of an organism are not directly visible at
conception, they emerge over the course of development, in a way not yet
understood but said to relate mainly to DNA driven processes. These are
shaped to some extent by environmental interactions, but the extent of
this on the morphology seems limited in practice. Yet we must recognise
that DNA itself does not 'drive' anything. It is a passive molecule, an
archive, containing (replicated) information on how to create proteins
(genes - ingredients) or sets of proteins (chromosomes - shopping
lists). There are no structural specifications present, no
organizational information - that has to arise by self-organization
along with the other cell components (about 500 metabolic processes,
involving 10,000 proteins, occur in each cell).

Explaining Form

"For my purposes a genetic replicator is defined by reference to its
alleles, but this is not a weakness of the concept. Or, if it is deemed
to be a weakness, it is a weakness that afflicts the whole science of
population genetics, not just the particular idea of genetic units of
selection. It is a fundamental truth, though not always realized, that
whenever a geneticist studies a gene 'for' any phenotypic character, he
is always referring to a difference between two alleles... The genes
that exist today reflect the set of environments that they have
experienced in the past. This includes the internal environments
provided by the bodies the genes have inhabited, and also external
environments, desert, forest, seashore, predators, parasites, social
companions, etc.

.... when we are talking about development it is appropriate to emphasize
non-genetic as well as genetic factors."

Richard Dawkins, The Extended Phenotype, 1999, Ch. 5 & 6

We thus need to explain the origin of the various forms that can occur,
these 'emergent' properties. The neo-Darwinian viewpoint is that random
variations in the genes can explain this. Unfortunately this explanation
seems inadequate since it assumes that for any feature of the body
(phenotype) a matching variation in the DNA (genotype) can be found, in
other words there is a linear or near-linear correspondence between gene
and morphology - a continuum of possible expression, so that all
intermediate variations will be possible (the environment also affects
the parameters of course). But genes themselves are not 'optimized' by
selection, only the phenotype is affected directly. So any functional
equivalence (isomorphism) at genetic level will be just as valuable to
the system at the phenotypic level (as will any other equivalent way of
achieving the same end). In other words two different sets of genes (or
alleles) which give rise to the same selected 'trait', will have no
selective forces acting relative to each other. Is this likely ?

The genetic makeup of our DNA relies on codons, units of 3 base pairs
coding for amino acids. There are 61 codons possible (plus 3
'punctuation' codons), yet only 20 amino acids are produced. Thus given
a gene, coding for a small protein comprising 100 amino acids, we could
have (on average) 3 different codons for the same amino acid, and 5 x
1047 different genetic arrangements coding for the same protein ! Given
that many proteins will have similar selective or functional effects
(due to similar shape - their folding characteristics), we can see that
genetic variation, in itself, does not guarantee any phenotypic
variation on which selection may then act, there may be long periods of
stasis when nothing happens (exploration of what are called neutral
networks), before a mutation occurs that actually causes a phenotypic
effect.

Trait Constraints

When we look at actual organisms we see that features rarely occur in
continuous variants, there are discontinuities between species - the
intermediate forms are never found. Traditional views dismiss this
problem as the result of 'selection', yet it seems clear that many
features are difficult to relate to any type of 'selective advantage'
without highly implausible 'just so' stories. Ranges of features (e.g.
number of legs) are highly constrained, some patterns (e.g. odd numbers
of legs) seem never to occur, or to do so only in restricted phyla (e.g.
starfish). This implies restrictions on the search space possible, in
other words evolution is not entirely 'random', it has biases. Previous
history has 'locked-in' features which are now difficult to escape, i.e.
developmental constraints seem to prevent certain genetically driven
variations becoming viable.

Epistasis

There is however no single gene for any phenotypic 'trait', any more
than one single part runs a car. An expressed gene produces only a
single protein, which must then interact with many more cell components
before any effect is seen. A single mutation, of course, can destroy a
trait (just like a single part failure can stop a car), but cannot
itself create anything complex in isolation. The features of any system
are thus a complex inter-meshing of processes requiring multiple lower
level components. Traits are the result of combinations of genes
(polygeny) and a single gene can also affect many traits (pleiotropy),
i.e. genes perform multiple jobs and a job requires multiple genes.

"The dynamics of allele frequency change at a locus are greatly affected
by linkage and interaction with other loci. Selection for favourable
combinations of genes can create strong associations (linkage
disequilibrium) among alleles at different loci if they are tightly
enough linked. Different gene combinations may confer high fitness, so
that a population can evolve towards any of several or many stable
genetic compositions... but pleitropy and linkage disequilibrium, giving
rise to negative genetic correlations between the selected character and
other traits including fitness, reduce the response to selection, and
cause the character to return towards its original state if selection is
relaxed."

Douglas J. Fuyuyma, Evolutionary Biology, 1986, Ch. 7, Summary

In fact, some (perhaps many) genes comprise many alternative exons
(active sequences) which can be spliced (assembled) into a number of
variant proteins, and then used for different purposes in different
contexts or creatures. This form of structure is true for all complex
systems, the interactions are a 'many to many' (N:M) process, not an
hierarchical (1:N) control structure as traditionally envisaged. It is
essentially a highly nonlinear configuration, where feedback processes
(both positive and negative) interact. So how can these overall features
or traits arise, if neither selection nor genes are specific enough ?

Regulatory Networks

Luckily an alternative process can cast light on this dilemma. Genes
come in two main forms, expression and regulatory (some perform both
functions however). The expressive (or structural) genes are those that
actually create the cell proteins (structure or metabolism) by the
familiar process involving mRNA copies from the DNA and synthesis by
tRNA and Ribosome - these we can regard as the 'low level' genes. But
before a gene can be expressed it needs to be 'switched-on' and this is
a function of the genetic regulatory system, the 'high level' control
process for the cell. There is an analogy here with computer programming
where the 'low level' or machine-code operations are specific and
fragile, whereas 'high level' languages allow a modular approach, each
statement controls a functional set of associated 'low level'
operations. Low level genes are like the ingredients of a recipe, the
high level ones choose the recipe (but maybe don't specify the
quantities of each ingredient...). Gene networks therefore can be
regarded as 'sub-routines', called as and when required to implement
either low (ingredient) or high (recipe) level functions during the
essential developmental (cooking) stage - the 'time' dimension.

Thus three stages are necessary for our model, the reductionist
cataloging of protein parts (gene structures); the holistic specifying
of their interconnectivity (switching functionality); and the dynamics
through time of the resultant 'system' under environmental influences.
Regulation in genes is actually poorly understood as yet, but it is
known that a combination of activation and suppression switching
operations is involved (using what are called 'promoters'). A typical
gene has associated, on average, ten or so switches, combinations of
activation and supression by other proteins that lock onto the switch
sites, so a complex network of interacting proteins is almost always
required to start and stop a particular gene activation. In fact, the
combinatorial logic possibilities are almost infinite here (a single
gene has about 1000 control combinations, a mere 5 have 1015), so even
though all animals have basically the same set of genes (we share 99%
with the chimp) a few changes in the 'wiring network' can lead to
massive changes in function and form.

The regulatory genes (or 'transcription factors') will act in many
different ways at different locations during the developmental process
(depending on specific switch activations), and the most powerful of
these (called 'tool box genes', including the homeotic or Hox genes) can
activate very complex top level building blocks, e.g. trigger the
complete development of an entire limb at a certain location (and can
perform very different construction jobs within the same creature or in
different creatures, depending on local context and development stage,
eg. limbs, eyes, heart or wings !).

If we simplify this process a little then we can represent it by a
system of logic gates. The epistatic (nonlinear) interactions between
genes can then be seen as interconnections between their regulatory
mechanisms, so in this way we can envisage a large scale network of
logical controls determining the DNA expression process.

Punctuated Equilibria

One feature of such a 'Boolean Network' is that expression doesn't take
place in a linear fashion, with gradual changes, but operates in jumps.
Cascades of interactions switch the expression sequence between
alternative stable modes (called attractors). Each mode flows through a
series of cyclic changes as each node (gene) in the sequence activates
or de-activates in turn (several genes will generally express at the
same time here, since each network consists of a modular number of
associated 'low level' units).

The net result of this is that the operation of the cell changes in
discrete steps, not incrementally. If we imagine a mutation affecting
not an expression gene (protein) but the switches of a regulatory
pathway then we have a mechanism based on complex system theory to
explain discontinuous variation (without disruption to the functional
integrity of any expression gene). A step change in cellular operation
could lead to a new type of cell (tissue) and the resultant development
to a new species. We can view mutation here as a two path process,
regulatory genes give step changes in function whilst expression changes
'fine tune' and optimize the current function. The 'gradualism' of
Darwin is no longer valid in all cases, 'saltationism' (step change) is
demonstrably involved also - both methods co-exist.

Phenotypic Development

Mechanisms for creating phenotypes during development however are still
unclear, since in this case we have the added complication of
multi-cellular organisation, together with the detailed way in which all
the cells grow and differentiate. Yet we do know that even single cells
communicate extensively (exchanging signals - physically, electrically
and chemically) so we perhaps have here a further interconnection and
regulatory network that may prove amenable Basins of Attraction to
similar reasoning - organs as attractors ? It has been found, from
simulations, that the attractor types that are seen can change, if
several cells are able to communicate. These cases correspond to richer
interconnection regimes and allow new types of attractor to exist that
cannot, it seems, occur in isolated cells. In some cases the entire
system can move spontaneously to a single type of new cell, or to a
stable mixture of cell types. These systems can be self-regulating, the
balance between types being a probabilistic feature of the interactions,
cells will change apparently at random until the correct, stable,
balance is seen.

This cellular example shows that the functionality of a group of cells
can proceed very well without external influence (we will allow the need
for non-specific flows of resources here, e.g. energy), the 'emergent'
form is a self-organized one, not dependent upon environmental
selection. Changes to the components of the cell (due say to mutation),
will change the balance of the system and the parts will then coevolve
(we can call this an internal selection) until a new balance is reached,
a new stable attractor - a cellular ecosystem. Note that the attractor
is a combined feature of the parts - it is not generated by parts in
isolation, thus molecular reductionism is an inadequate analysis
technique with which to explain the whole in such complex systems.

Whole Systems

Adaptation studies, in general, tend to focus upon individual 'traits',
culling specific failures (or selecting 'improvements') e.g. giraffe
neck length, in turn irrespective of other co-existing 'superiorities'
(i.e. each 'mutation' is assumed to occur sequentially, and they are
selected or rejected in isolation over multiple generations). The more
complex the organism becomes however the more traits exist that can
interact to affect the overall performance (so survival may be a very
nonlinear optimization process), e.g. giraffe leg length is important
too, the traits aid or oppose each other in fitness terms. Each of these
observable traits has emerged in some way from the overall interactions
of their parts, in ways not currently known in detail. Genes interact
extensively as we saw (epistasis - polygeny and pleiotropy), so it seems
generally inaccurate to assign particular properties (traits) to an
isolated proportion of the lower level components of a system
(especially to single genes). Likewise, there can be multiple paths
through the same genetic sub-routines, dependent upon environmental
influences, so the genotype needs to be considered instead from an whole
systems perspective, as an emergent dynamic whole with multiple possible
stable attractor states.

Emergence

So what is this emergence exactly ? Generally it is defined by saying
'the whole is greater than the sum of the parts'. In other words we
cannot predict the outcome from studying only the fine details. Examples
include cellular metabolism, ant colonies, organism development,
snowflakes. Of course 'knowing' the outcome we can develop reductionist
explanations for explaining (to some degree of probability) the small
scale interactions involved - this is a one to many process, we break
down the trait into multiple isolated parts or sets of parts. The
reverse process, many to one -CA Music in other words explaining from
first principles what actual forms will appear - seems beyond us. The
essence of the phenomena however is that 'new' descriptive categories
are necessary, in other words the features or attractors cannot be
described within our existing vocabulary, we require new terms, new
concepts to categorise them. This is a feature of 'open-ended' evolution
- 'novelty' appears outside our current experience or that of the
system. In these cases we cannot easily apply a 'fitness function' since
the 'function' is initially unknown (and may not even exist) and is
highly context dependent.

Discarding Dualism

It is useful here to consider the relevance of dualism to emergence. It
may be considered that by saying that emergent properties are not
'explicable' by consideration of the lower level details, that we are
claiming that there is an inherent duality between the levels of
description (rather like that claimed by Descartes between body
functions and those of mind). That is not the case. What we are saying
is that there are a number of nested levels of detail, each of which has
properties different from those levels that comprise it, and so needs a
new holistic type of description or label to be applied (one that cannot
be stated in terms of the individual part properties, neither separately
nor in other partial combinations).

There are three aspects involved here. First is the idea of
'supervenience', this means that the emergent properties will no longer
exist if the lower level is removed (i.e. no 'mystically' disjoint
properties are involved). Secondly the new properties are not
aggregates, i.e. they are not just the predictable results of summing
part properties (for example when the mass of a whole is simply the mass
of all the parts added together). Thirdly there should be causality -
thus emergent properties are not epiphenomenal (either illusions or
descriptive simplifications only). This means that the higher level
properties should have causal effects on the lower level ones - called
'downward causation', e.g. an amoeba can move, causing all its
constituent molecules to change their environmental positions (none of
which however are themselves capable of such autonomous trajectories).
This implies also that the emergent properties 'canalize' (restrict) the
freedom of the parts (by changing the 'fitness landscape', i.e. by
imposing boundary conditions or constraints).

Despite the different labels we give to emergent properties at the
different levels (e.g. cell, organism, society) , the general features
found at each level are considered equivalent in complexity terms, each
being due to the same form of connectivity applied within the specific
space and time framework appropriate to that form of structure. The
semantic labels are level (function) dependent, the emergence features
are considered universal under the 'general systems theory' viewpoint
underlying complexity science (i.e. the 'laws' apply to all equivalent
forms of systems, regardless of material or immaterial form). By
studying the lower level connectivity of each system we can, in
principle (if not always in practice), determine the expected emergent
features, and conversely by relating the emergent features to those of
systems whose connectivity is not known we may be able to infer their
internal connectivity also. This is where the science comes in, by
allowing us to model, in computer simulations, various connectivity
options and determine which transition rules/interactions are critical
to the emergence of certain features and which are not.

Hierarchical Levels

For our purposes here we need not be concerned about the technical
details, but we do need to be aware that self-organizing emergence is an
hierarchical process. Sub-atomic particles give rise to Atoms (which
have emergent properties - e.g. density), these in turn combine to form
Molecules which have different emergent properties (e.g. shape), which
in turn form Metabolisms with yet more properties (e.g. cycles), which
constitute Cells with further properties (e.g. movement), and then to
Organisms at a yet higher level (goals) and on to Humans (abstractions).
These levels cannot easily arise by means of standard mutation and
crossover operations but seem to require a new form of evolution,
sometimes called 'compositional evolution', 'cooperative coevolution',
'synergistic selection' or 'holistic darwinism', a symbiotic form that
allows separately evolved functional building blocks to combine in
modular fashion, improving overall combinatorial fitness.

In a similar way we need to ask to what extent can even higher level
interactions self-organize and what is the influence of selection in,
say, an ecosystem. Here we return to our initial distinction between
external and internal processes. For our predator/prey interaction the
predator was regarded as an external selective force on the prey
behaviour (itself now regarded as a self-organizing phenotype). Yet we
can also regard this from a higher level, as an ecosystem, where the
interactions between the constituents are then internal to the system.
We now have a self-contained coevolutionary system, similar to our cell,
and the system will evolve over time to form a balance, an Evolutionary
Stable Strategy (ESS).

Gaia and Self-Regulation

Taking a further step upwards, the whole planet is interconnected by
weather, birds, insects etc., so we could regard that in turn as a
coevolving organism - the Gaia theory. Again on a Solar System or
Galactic level interactions of a different form (gravitational and
electromagnetic) lead to emergent structure, suggesting that the concept
of 'external selection' is simply a convenient simplification in what is
always essentially a two way process. Self-regulation by feedback
mechanisms seems to be a feature of every level of evolution, a
hierarchy of order, emergent from initial disorder.

Teleology and Teleonomy

We now come to the matter of 'teleology', the following of goals in
evolution and behaviour and the relationship of this to genes. Crucial
to such a concept is the idea that humans, animals and perhaps even
plants are causally effective, i.e. that they are active agents and not
just passive ones. As we have seen, emergent properties allow for such a
downward causation scientifically, and it proves to be philosophically
incoherent to deny our own causality as humans (e.g.' who' is causing
the self-referential denial?). Science has however traditionally refused
to allow a role for non-random directions in evolution (the appearance
of such, i.e. 'teleonomy', does not prove such goals exist), yet there
are clear parallels between human self-organizing behaviours (cultural
norms) and those of 'lesser' animals, both affect their evolutionary
dynamics by their behaviours, in ways that do not seem random. The
problem as usually stated is that the inheritance of any such 'learned'
behaviours (as proposed by Lamarck) seems impossible, there is no
mechanism to incorporate such changes into the genes and only the
reproduced genes (not the body) in fact survives (but note this doesn't
necessarily apply in some asexual phyla). This limitation can be shown
to be false to some extent, an indirect mechanism is known to occur
called the Baldwin effect - in which a change in behaviour provides a
selection bias making such (originally learnable) behaviours more
genetically determined in later generations. But that is not our concern
here, we can instead allow that genotype structures do not change in
themselves with learning, but claim that our behaviour can and does
change their expression sequences, i.e. those regulatory pathways.

What we need to consider also is that since one species (Homo sapiens)
can clearly change its place in its coevolutionary environment, in ways
not directly related to its genes but by deliberate cultural activities,
then might this not be true for other species also ? Any form of
available choice allows an animal (or plant) to alter the selective
forces it experiences (and to a large extent those experienced by its
offspring also). Grazing by sheep moves them from an area of scarce food
to one of plenty, clearly reducing the selective pressures on them -
their cultural 'choice' (flocking), conscious or not, increases their
collective fitness as a group relative to other possible choices.
Survival and selective reproduction then are closely associated with the
coevolution of organisms and environment, and dependent not only upon
genes but on experiences (trial and error learned behaviours) also. This
is important because the fitness landscape is not homogeneous (the same
everywhere) but heterogeneous (it has spatial and temporal structure).
This allows different behaviours to search out different niches,
alternative lifestyles or formulae for success, and much faster than is
possible by genetic variation alone. In this way culture transforms
'group selection' from being competition between spatially separated
groups, to being competition between temporal choices, possible
bifurcations in group trajectories, the poorer choice being selected
against by immediate environmental feedback - including the emergent
downward causation of group behaviour. General Selection Theory
recognises that the basic principles of natural selection (variation,
selection, retention) apply at all levels of reality, not just to genes
or to biological individuals, thus small or large group 'learned'
behaviours have adaptive effects also.

Lamarkian Learning

Learning isn't however just a human or higher animal prerogative, it is
known to occur in simple nematode worms (which are brainless, with
exactly 302 deterministically wired neurons), and even in single-celled
bacteria. Passing messages between members of the species is also not a
function of supposed 'intelligence', slime molds are quite good at it.
Since we assume that our 'learning' is (variously) stored chemically, by
physical cellular or neuronal changes, or by accessible parts of our
environment then all these possibilities for (external or internal)
environmental plasticity affecting gene expression seem open to any
lifeform, however simple, i.e. nurture drives nature as well as the
other way about, they must co-evolve (in fact hundreds of such enabling
or disabling signals of various types are constantly passing between
cells and/or organisms, with more being discovered each year). What this
means in practice is that our changing environmental context is found to
actively select gene activity, it determines which genes are expressed
and which behaviours are generated - which then in turn determine our
next environmental context and the subsequent genetic processes. This
mutual triggering effect is the 'structural coupling' of autopoietic
thought and is an active and increasingly recognised area of modern
biological research.

Could a simple learned emergent property however be passed on directly
in any other way, generation to generation (non-culturally) ? For simple
cells, using asexual reproduction, passing chemical knowledge in this
way may well be possible - bacteria pass on antibody resistance in a
similar way. For multi-cellular organisms this is more problematical,
learning presumably affects the somatic (body) cells not the gametes
(specialised reproductive cells), yet in these cases also the chemical
environment is common to all cells, leaving some possibilities open e.g.
the child's immune system 'learning' to recognise foreign bodies from
the mother's and the mother's chemistry affecting embryo development (as
seen in thalidomide cases).

Conclusion

To some extent or another evolution is affected by the decisions made by
the lifeforms comprising it, we change our destiny (say) by moving to a
warmer climate or by deciding to scavenge. Such active decisions
(conscious, unconscious or random as the case may be) change the shape
of our fitness landscape, and this in turn alters that of all the
associated species. Even by digging a hole we alter the environment,
changing the landscape for other creatures (literally in this case !),
so we cannot study evolution on the basis that the fitness landscape is
fixed and not altered by the organisms present, the full two-way
coevolutionary perspective is always necessary. The concept of genetic
'selection', useful though it is in an isolated sense, can now be seen
as just a passive simplification for what is always a complex,
coevolutionary and adaptive emergent system. This system makes use of
dynamic self-organizing processes and selection at many levels
(chemical, regulatory, learning, coevolutionary) and needs to be
understood in a rather deeper sense than the shallow linear reductionism
often employed by neo-Darwinists. The realisation that this is so has
led to the new field of Evolutionary Development Biology (Evo Devo for
short), to which we would add the power of self-organization and
attractors. Let's leave the last word however to paleontologist Stephen
Jay Gould:

"In any environment, hundreds of possible anatomies might work - and the
forms and colours of this particular population in that specific valley
are fortuitous consequences of the largely non-adaptive mutations that
happened to arise and spread in an isolated population.

The resulting pattern of differences among valleys is largely
non-adaptive. Each local race must avoid elimination by natural
selection (and is fit in this negative sense), but its particular
features represent only one in a myriad of workable possibilities, and
any particular solution arises by the happenstance of mutation in an
isolated population, not by natural selection."


https://archive.is/BMtQd#selection-127.0-542.0








--

"To paraphrase the Buddha — Three things cannot be long hidden:
the sun; the moon; and the truth. ‬

“But let justice roll down like waters and righteousness
like an ever-flowing stream” Amos 5:24

~ Former FBI Director James Comey (12-1-17)


s

[*Hemidactylus*]

Bauplane are old hat. Jonathan is just getting around to this way of
thinking? He has a lot of catching up to do to match my knowledge.

Saltation existed long before complexity theory and punctuated equilibrium
is not saltation. We’ve been down this road before.

Susumu Tonegawa used molecular reductionism to give us a better
understanding of how our immune system works and subsequent knowledge
attained about rearrangement/hypermutation in lymphocytes is the best
example of intraselection. Bullshitting emergentists such as jonathan know
nothing about that.

To what extent is emergence a reflection of our epistemic limitations
rather than ontological reality? Would Laplace’s demon believe in
emergence? Chaos and chance could be beyond the demon’s grasp.

Gaia is nonsense that takes emergence too far.

>
> Teleology and Teleonomy
>
> We now come to the matter of 'teleology', the following of goals in
> evolution and behaviour and the relationship of this to genes. Crucial
> to such a concept is the idea that humans, animals and perhaps even
> plants are causally effective, i.e. that they are active agents and not
> just passive ones. As we have seen, emergent properties allow for such a
> downward causation scientifically, and it proves to be philosophically
> incoherent to deny our own causality as humans (e.g.' who' is causing
> the self-referential denial?). Science has however traditionally refused
> to allow a role for non-random directions in evolution (the appearance
> of such, i.e. 'teleonomy', does not prove such goals exist), yet there
> are clear parallels between human self-organizing behaviours (cultural
> norms) and those of 'lesser' animals, both affect their evolutionary
> dynamics by their behaviours, in ways that do not seem random.

Teleonomy is apparent goal directedness granted by possession of a genetic
recipe crafted by generations of selection. Ernst Mayr wrote of such things
decades ago.

> The
> problem as usually stated is that the inheritance of any such 'learned'
> behaviours (as proposed by Lamarck) seems impossible, there is no
> mechanism to incorporate such changes into the genes and only the
> reproduced genes (not the body) in fact survives (but note this doesn't
> necessarily apply in some asexual phyla). This limitation can be shown
> to be false to some extent, an indirect mechanism is known to occur
> called the Baldwin effect - in which a change in behaviour provides a
> selection bias making such (originally learnable) behaviours more
> genetically determined in later generations.

The Baldwin effect is an ancient concept. I think we have been down this
road before where jonathan copypastes ideas of which he has demonstrated
zero understanding.

>But that is not our concern
> here, we can instead allow that genotype structures do not change in
> themselves with learning, but claim that our behaviour can and does
> change their expression sequences, i.e. those regulatory pathways.
>
> What we need to consider also is that since one species (Homo sapiens)
> can clearly change its place in its coevolutionary environment, in ways
> not directly related to its genes but by deliberate cultural activities,
> then might this not be true for other species also ?

Has jonathan gotten off his lazy ass and learned anything about lactase
persistence in some human populations?

Is any of this purposeful striving? Or fortuitous happenstance?

>
> Conclusion
>
> To some extent or another evolution is affected by the decisions made by
> the lifeforms comprising it, we change our destiny (say) by moving to a
> warmer climate or by deciding to scavenge. Such active decisions
> (conscious, unconscious or random as the case may be) change the shape
> of our fitness landscape, and this in turn alters that of all the
> associated species. Even by digging a hole we alter the environment,
> changing the landscape for other creatures (literally in this case !),
> so we cannot study evolution on the basis that the fitness landscape is
> fixed and not altered by the organisms present, the full two-way
> coevolutionary perspective is always necessary.

Didn’t you followup to my asking you to learn more about Sewall Wright and
adaptive landscapes with some insult about my being out of date?

> The concept of genetic
> 'selection', useful though it is in an isolated sense, can now be seen
> as just a passive simplification for what is always a complex,
> coevolutionary and adaptive emergent system. This system makes use of
> dynamic self-organizing processes and selection at many levels
> (chemical, regulatory, learning, coevolutionary) and needs to be
> understood in a rather deeper sense than the shallow linear reductionism
> often employed by neo-Darwinists. The realisation that this is so has
> led to the new field of Evolutionary Development Biology (Evo Devo for
> short), to which we would add the power of self-organization and
> attractors.

Evodevo ain’t that new. But Jonathan probably doesn’t know that. Copypaste
and knowledge are different things.

> Let's leave the last word however to paleontologist Stephen
> Jay Gould:
>
> "In any environment, hundreds of possible anatomies might work - and the
> forms and colours of this particular population in that specific valley
> are fortuitous consequences of the largely non-adaptive mutations that
> happened to arise and spread in an isolated population.
>
> The resulting pattern of differences among valleys is largely
> non-adaptive. Each local race must avoid elimination by natural
> selection (and is fit in this negative sense), but its particular
> features represent only one in a myriad of workable possibilities, and
> any particular solution arises by the happenstance of mutation in an
> isolated population, not by natural selection."
>
>
> https://archive.is/BMtQd#selection-127.0-542.0
>

Is any of the above original thought added by you?

[Jonathan]

Dude, this essay is an introduction, of course it'll
touch on preexisting ideas, I mean jesus christ
your desperate to complain.

Gould, 1979[edit]

Stephen J. Gould explored the idea that the different phyla
could be perceived in terms of a Bauplan, illustrating
their fixity. However, he later abandoned this idea
in favor of punctuated equilibrium.[6]
https://en.wikipedia.org/wiki/Body_plan

Good grief, before Darwin most believe in the
step changes of saltationism.

After Darwin most believed in gradualism.

Complexity theory says both occur, step changes
and gradualism.

https://en.wikipedia.org/wiki/Saltation_(biology)#History

You're still living in the last century.

Stanford Encyclopedia of Philosophy
Notes to Reductionism in Biology

“The molecular reductionism that dominated twentieth-century
biology will be superseded by an interdisciplinary approach
that embraces collective phenomena”
https://plato.stanford.edu/entries/reduction-biology/notes.html


Complexity science and emergence are ALL ABOUT
collective phenomena, and ALL ABOUT an
interdisciplinary approach.

A relentless theme of complexity science is
reductionism is no longer enough, but only half
an explanation, the macro or collective properties
~(emergence) is the other half

Please keep in mind this science is about
how the parts /interact/, not about the parts.

I ask others to answer this question to get at
yours.


When emergence is seen in a system what assumptions
can be made about the parts of the system?



Whenever emergent properties are seen, that means
it's parts must be critically interacting, or
acting...chaotically.

The demon dies whenever a system has self organized
or is evolving, as the parts must stand at the
transition between order and disorder, or
between static and chaotic behavior.

You can't precisely define the position
or movement of the parts at any given
time if emergence is being produced.

Or as our knowledge of the whole increases
(becomes self organized or evolved) our ability
to know the parts in detail decreases.

So by moving up in complexity, as opposed
to reducing to parts, our ontological
knowledge increases while our epistemic
limitations increase.

But keep in mind this is a 'relativistic' view.

In the relationship between society and person
the society behaves simply, while the people
are complex.

But in the relationship between a person
and it's components, the person behaves simply
while it's parts behave chaotically.

Which is defined to be the part and which is
defined to be the whole must be defined in
advance by the observer before applying
complexity principles.

This is a huge source of confusion.

The point with Gaia is everything is connected
and that's true, so in theory to define anything
we have have to define everything /at the same time/.

A clear contradiction and impossibility.

Which is the problem with the coevolutionary
relationship between environment and life.

This contradiction is /at last solved/ by using
the concept of emergence.

We define the 'emergent' whole in order to
define the parts.

We reverse our scientific world view, and again
this is a huge problem with selling the idea
to long held reductionist mindsets.

But this is the only way forward, the only
way to hurdle all the remaining brick walls
of objective methods.

The concept of emergence is just now taking shape.
There are four general classes of emergence.

You have to carefully read the entire essay at
the link below to understand the modern view of
emergence and it's centrality to the future
of science in general, and especially
nature.



Types and Forms of Emergence

(excerpts)

4. Taxonomy
4.1 A New Taxonomy


Type I Simple/Nominal Emergence
without top-down feedback

Type Ia Simple Intentional Emergence
(machines, software)
Type Ib Simple Unintentional Emergence
(thermodynamic properties, avalanche)



Type II Weak Emergence
including top-down feedback



Type IIa Weak Emergence (Stable)
(foraging, ant colonies, flocking)
Type IIb Weak Emergence (Instable)
(bubbles and crashes, fads, social unrest)


Type III Multiple Emergence
with many feedbacks

Type IIIa. Stripes, Spots, Bubbling
(stock markets, pattern formation)

Type IIIb. Tunneling, Adaptive Emergence
(puctuated equil, scientific revolutions)


Type IV Strong Emergence
(life, mind, ideas)


The macroscopic level is independent from the
microscopic level, because there is a mesoscopic
or intermediate level that protects and isolates
the one from the other. Therefore in strong emergence
the macroscopic level is irrelevant to the microscopic
level and vice versa.

The macroscopic level remains invariant if the
micoscopic level is replaced by something else,
as long as the mesoscopic or intermediate levels
remains the same. Laughlin calls this the
“Barrier of Relevance”.

Strong emergence in this sense is the crossing
of the barrier of relevance. It is often related
to very large jumps in complexity and major
evolutionary transitions,



4.2 Different perspectives

The classification can also be seen from a
different perspective, if it is specified
in terms of constrained generating processes
or roles:

type I corresponds to fixed roles,

type II to flexible roles,

type III to the appearance of new roles and
the disappearance of old ones,

type IV to the opening of a whole new world of
new roles.

Another classification possibility is to use different
levels of prediction:

intentional emergence of type I is predictable,

weak emergence of type II is predictable in principle
(though not in every detail),

multiple emergence of type III is chaotic or not
predictable at all,

strong emergence of type IV is not predictable in principle.

http://old-classes.design4complexity.com/7701-S14/reading/critical-thinking/Types-and-Forms-of-Emergence.pdf

I gotta run, but I have to say this is the first
genuine or science minded reply I've gotten
in this ng in a long time.

Thanks for replying and Merry Chris...ah I mean
Happy Holidays~

[T Pagano]

This is one of the best summaries I've seen here or elsewhere. Thanks
for providing it.

On Sat, 23 Dec 2017 09:55:51 -0500, Jonathan wrote:

> Emergence and Evolution - Constraints on Form by Chris Lucas
>
>
> "The view of evolution as chronic bloody competition among individuals
> and species, a popular distortion of Darwin's notion of 'survival of the
> fittest,' dissolves before a new view of continual cooperation, strong
> interaction, and mutual dependence among life forms. Life did not take
> over the globe by combat, but by networking."
>
> Lynn Margulis and Dorian Sagan, Slanted Truths, 1997
>
> "The emergent qualities that are expressed in biological form are
> directly linked to the nature of organisms as integrated wholes; these
> can be studied experimentally and simulated by the use of complex
> non-linear models."
>
>

snip