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EME: Biological Examples

EME 2008
Biological emergence
• Emergence is studied in biology for two reasons:
– To try to understand the biological mechanisms
– To apply biological mechanisms (or their analogies) in
engineered systems
• Biological emergence helps understanding on a
practical level
– but may cloud definitions of emergence

EME 2008
Life cycle examples
• Slime moulds and fungi
– Environmental factors trigger change in form and function
– Collective activity as a route to species survival
• Emergence is relevant in many ways
– Emergence of various multi-cellular behaviours in a group of
amoebae
– Emergence as a factor in evolution
• Contributes understanding of
– Simplicity
– Power of environmental triggers
– Differentiation among superficially identical agents

EME 2008
Construction and organisation
• Social insects such as wasps, bees, ants, termites
– Build and maintain complex nest structures
• invisible and incomprehensible at scale of individual insects
• essential to survival
– Achieve elaborate task differentiation without co-ordination
– Efficient group foraging and navigation behaviours
• Emergent structures
– Physical and social organisation
• Contributes understanding of
– Group co-ordination through local interaction
– Simple behaviour rules
– Discrete and continuous environmental influence (stigmergy)

EME 2008
Moulds and Fungi
emergence of multi-cell behaviour

http://herbie.ucsd.edu/~levine/dicty.html

EME 2008
Slime moulds
• Focus on slime moulds
– Extreme example, but similar group behaviour occurs in, eg.,
fungal mycelia
• Two phyla
– Dictyosteliomycota (dicytostelids)
• Primarily in soil
– Acrasiomycota (acrasids)
• On dead plant parts, tree bark, dung and soil
• Both exhibit single-celled amoeba and multi-celled
proto-organism behaviour

EME 2008
Slime mould life cycle
Spore dispersion
Dyctyoselium xxx?
Single spore
becoming an
amoeba

Acrasis rosea

http://dictybase.org/Multimedia
Starvation /LarryBlanton/dev.html
response

Stalk-sporing demarcation
after Olive, The Mycetozoans, 1975

EME 2008
Dicytostelids
• First discovered in 1869 by Oskar Brefeld
• Three genera, 50 species
• Dictyostelium discoideum isolated by Raper (1935)
– important model organism for study of
• Cytokinesis (division of cell cytoplasm)
• Motility (spontaneous movement)
– chemotaxis, phototaxis, thermotaxis (move in response to
chemical, light, heat)
• Phagocytosis (ingestion by incorporation in another cell)
• Cell signalling, cell sorting and cell-type determination

Carris, General Mycology, http://classes.plantpath.wsu.edu/plp521/


DictyBase http://dictybase.org/dicty.html
http://herbie.ucsd.edu/~levine/dicty.html

EME 2008
Slime and time
• Single-celled amoebae with a will to survive
• A billion years of evolution
– Adaptation to periodic starvation conditions
• Three life cycle stages
– Distinct single-celled entities
• Do all the things single-celled amoeba usually do
– Slug-like multi-cellular mass
• Behaves like a slug, moving to favourable sites
– Fruiting body development and dispersal
• Like a fungus

Bonner, Evolution and Development, v5(3), 305-313, 2003

EME 2008
The things amoebae usually do
• Amoeba feeds on local food source
– Bacteria on decaying organic matter in soil
– Self-reproduce independently

• When food runs out, such amoebae usually form a


passive spore or cyst
– Dispersed by water or hitching-a-lift
– Chance location of more food

EME 2008
Evolutionary disadvantage
• Slime amoebae can turn into individual cysts
– as a defence to damaging conditions
• But a passive response is not conducive to species
survival
• Cyst stage has evolved into clustering behaviour
– Akin to herding for collective preservation
– or perhaps to attract predators responsible for spore
dispersal (nematodes)
• Cluster is able to move further, faster, and more
reliably than cysts
Bonner, Evolution and Development, v5(3), 305-313, 2003

EME 2008
How to form a slug
• Starvation causes a few auto-cycling amoebae to emit
pulses of cAMP
– cyclic adenosine monophosphate
• Other starving amoebae become receptive to cAMP,
and move towards its source, also emitting cAMP
– streams form, moving to auto-cycling amoebae

• A mound of amoebae develops and eventually slumps


to form a “slug”

• The “slug” moves towards light and heat


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Slime mould movement
• Dicty “slug” contains 10-50 000 amoebae in a cellulose
sheath
• Cell sorting:
– Amoebae differentiate into pre-spore and pre-stalk cells
– Pre-stalk cells form the active moving area at the front
– Mainly pre-spore cells at the back
• Individual pre-stalk cells move around within the slug
• Motion is a series of compressions and extensions

Williams et al, Cell migrations during


morphpgenesis, BioEssays v5(4), 1986

EME 2008
Emergent behaviour of “slug”
• Once formed, “slug” behaves as multi-cell organism
– Physiological responses move it towards a suitable
reproduction site
– Sensitivity to chemical gradients develops at what becomes
the front
• Each amoeba still acts as an individual
– What it does depends on where it is in the cluster
• Amoebae become more cyst-like at the rear
• (or is it that cyst-like amoebae end up at the rear?)
– Some amoebae change role to maintain the overall slug
characteristics
• Pre-stalk amoebae can change to pre-spore during movement

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Fruiting
• “Slug” moves to find a good place to spread spores
– Not to find new food sources
• Light and humidity are monitored
– Looking for open, airy site
• Once suitable site located, fruiting phase begins

EME 2008
Dicty slug to fruiting body
Spores
after Carris, General Mycology,
http://classes.plantpath.wsu.edu/plp521/

~80%

Cells in anterior
direct movement Cells in posterior
become spores

Cellulose sheath
~20%
secreted by
amoebae
Direction of movement

EME 2008
Multi-cell evolution?
• Spore and stalk amoeba are both viable
– Only a superficial division of amoebae by role
• This is a primitive form of social organisation
– might be an evolutionary link from single-celled to multi-
celled organisms
• Study of different slime moulds contributes to study
of evolution
– Multi-cell organisms, social organisation
• Amoebae self-organise and new structures emerge
– Is emergence necessary for evolution?

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What can slime mould do for CS?
• Studies of Dicty and its environment contribute to
understanding complex systems
– Dicty respond to light, temperature, oxygen and ammonia
gradients
• Computation and engineering need to understand the
role of the environment in emergent systems
– Specific cases
– General influences

EME 2008
What can slime mould do for CS?
• Dicty has well-developed cell-sorting self-
organisation
– Fungal mycelia appear to have similar mechanisms
• Computation and engineering need to understand how
simple systems can change characteristics and roles
in response to need
– Autonomous systems
– Dependablity
– Artificial emergent systems

EME 2008
What can computation do for biology
of slimes, fungi etc?
• Traditional modelling
– Heavy-duty computation for solving differential equations
that model the observed changes over time and space
• A model that uses complicated equations to reproduce observed
behaviour and structures
• Emergent modelling
– simulating systems of basic components and exploring how
the observed behaviour emerges
• Models that can be tailored to reproduce the emergence
• Models that biologists can experiment with
• Early stages for emergent modelling
– Proposals for research programs; student projects etc.

EME 2008
A plug for a project (FACP/1)
• Fungal mycelia are not unlike multi-cell slime mould
– Three forms of particulate biomass
– Leading particles most active and “cause” motion
– Biomass changes role according to environment
• Traditional modelling uses 10 parameters and four
differential equations
• What if we just model lots of biomass particles and
see what happens?

http://www-users.cs.york.ac.uk/~fiona/projects2008.html
Falconer et al, Biomass recycling and the origin of
phenotype in fungal mycelia, Proc. Royal Soc. B, 2005

EME 2008
Construction by wasps, termites,
and ants
Emergence of physical and social structures

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Construction theories in biology
• Social insects construct
– Complex nest structures
– Social organisation structures
• Early studies assume that complex behaviour or
structure implies complex intelligence
– Wasp with blueprint for whole nest (Thorpe, 1963)
– Termites with individual copies of the plan for the mound
– Ants with excavation schedules
• Now it is agreed that construction is guided by simple
rule application, in response to environmental stimuli

EME 2008
Paper wasps
2 cm

200 Polistes species create hexagonal


combs of dried plant fibres and saliva,
attached at the back by a pedicel

http://en.wikipedia.org/wiki/Paper_wasp

EME 2008
Social wasp nests
• Nests for rearing larvae
– Up to a million compartments per nest
– Each Polistes species’ nest has different dimensions, but
similar construction
• New nest is started by a single female
• attaches the pedicel and the first few cells
– Increasing number of wasps contribute cells
• Preference for filling in gaps and completing rows

Bonabeau et al, Swarm


Intelligence, 1999, ch 6

EME 2008
Nest development

By this stage, almost any move will


create favourable construction sites
and the nest will grow quickly

EME 2008
Science and nest form
• Early research asserted an ancestral form and a
developed form, but no general agreement:
ANCESTRAL ADVANCED
Single cells or string of Symmetric radial form
individual cells
Round nest with broad base Pedicellate nests with asymmetry
Pendant comb Symmetric round nest
• Subsequently shown that simple architectural rules
may account for all known nest forms
Karasi and Penzes, Nest shapes…, Proc. Royal Soc. B, v265, 1998
Bonabeau et al, Swarm Intelligence, 1999

EME 2008
Wasp construction modelling
• Learning about construction by simulation of supposed
architectural models
– Observed preference for filling rows
– Prefer to build a new cell where three sides exist
• Probabilisitic rules

• Parallelism constrained by architecture


– Limited number of places for wasps to work at any size
• Models how wasps might apply rules
– Simulate stigmergy and behaviours that it prompts

EME 2008
A reminder of stigmergy
…process by which the results of an insect’s activity
act as a stimulus to further activity (OED 2nd edn)

• Not just restricted to insects


– Agent activity changes its environment
– Agents respond to state of the environment
– Actions are coordinated through the environment

EME 2008
Two forms of stigmergy
• Discrete or qualitative stigmergy
– Specific signs that stimulate or suppress behaviours
• Given a set of stimuli { Xn }, stimulus Xi results in specific
response xi
• Response xi can change stimulus Xi to stimulus Xj
– if … then … else rules as in wasp nest construction
• Continuous or quantitative stigmergy
– Continuous signals such as chemicals, temperature, light
– Response at threshold or in proportion to amount of stimulus
• Response can enhance or suppress signal strength
• Can have discrete and continuous together
– Different classes of response with quantitative stigmergy
defining specific response within each discrete class

EME 2008
Wasp nests and stigmergy
• Observation of wasp construction revealed that the
size and current form of the nest dictates the
probability of addition of a new cell
• This is discrete stigmergy
– Each wasp arrives at a particular part of the nest
• Observes characteristics of that part of the nest
• Constructs cell where it perceives a suitable gap
– Wasp perception is accounted for by probabilistic rules
• n% chance of filling in a gap between 3 existing cells etc
• Note that wasp perception also constrains the nest
– When the nest is small, many potential constructors cannot
find a suitable site to build a new cell

EME 2008