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Modeling and simulation of the fundamental principles of self-patterning
and self-assembly during embryonic development, with exportation to
artificial systems
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The spontaneous making of an entire organism from a single cell is
the epitome of a self-organizing and programmable complex
system. Through a precise spatiotemporal interplay of genetic switches
and chemical gradients, an elaborate form is created without explicit
architectural plan or engineering intervention. This original
study, which I designed and developed, proposes a multi-agent
simulation and exploitation of these fundamental morphogenetic
mechanisms.
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Overview
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On the one hand, natural phenomena of spontaneous pattern formation
are generally random and repetitive, whereas, on the other hand,
complicated heterogeneous architectures are the product of human
design. The only examples of self-organized and structured systems
are biological organisms produced by development. Can we export
their precise self-formation capabilities to computing systems?
This work proposes an "embryomorphic engineering" approach inspired
by evo-devo to solve the paradoxical challenge of planning
autonomous systems. Its goal is to artificially reconstruct complex
morphogenesis by integrating three fundamental ingredients:
self-assembly (SA) and pattern formation (PF) under
genetic regulation (GR).
It presents a spatial computational agent-based model that can be
equivalently construed as (a) moving cellular automata, in which
cell rearrangement is influenced by the pattern they form, or
(b) heterogeneous swarm motion, in which agents differentiate into
patterns according to their location. It offers a new abstract
framework to explore the causal and programmable link from
genotype to phenotype that is needed in many emerging computational
domains, such as "amorphous computing" or "artificial embryogeny".
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Bio-inspiration
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One of biology's modern challenges is to elucidate the genetics and
evolution of biological development, or "evo-devo", i.e., unify
organisms in a generative way beyond their seemingly endless
diversity of form. How do nonspatial gene interactions extend in
3-D space? My work schematizes and simulates some principles of biological
development using an expanding lattice of cells (Fig. c).
Each cell contains a genetic regulatory network (GRN), modeled as
a feed-forward hierarchy of switches that can settle in various
on/off expression states (Fig. a-b).
Local morphogen gradients (X, Y) provide positional
information in input, which is integrated by each GRN to produce
differential expression of identity genes (I, J, ...)
in output. Similarly to striping in the Drosophila embryo, the
lattice becomes segmented into spatial domains of homogeneous
genetic expression (one for each identity gene; Carroll et al. 2001)
that resemble stained glass motifs (Fig. d).
Meanwhile, it also expands by cell proliferation, creating new
local gradients of positional information within former
single-identity domains (Fig. d, right). Analogous to a growing
canvas that paints itself (Coen 2000), the alternation of growth and
patterning results in the creation of a form.
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Ultimately, more realistic details can be added by linking this
artificial model with biological studies that provide a close
observation and measure of multicellular behavior during
development. I recently collaborated in two large European projects,
Embryomics and Bioemergences, focused on automating the
morphodynamical reconstruction of the cell lineage tree underlying
the processes of animal embryogenesis. An organism's "embryome" is
defined as a description of the multiscale dynamics of the early
stages of development. Its reconstruction necessitates a paradigm
of systematic investigation of cell behaviors and lineage as a
branching process in space and time. Biologists produce and
annotate time-lapse series of organism development, while
mathematicians and computer scientists process these images to
reconstruct and model cell dynamics.
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Toward artificial development
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This study attempts to reproduce morphogenesis through a
multiscale and modular distributed process.
Abstracting from biological development, an important goal is
to contribute to a novel engineering paradigm of system assembly
that would replace omniscient architects with large-scale
decentralized collectivities of agents.
Various research works have investigated the possibility of obtaining
self-formation capabilities from a variety of complex computing
systems. Since functionality is distributed over a great number of
components, it would be an insurmountable task to assemble and
instruct each of them individually. Rather, in a way similar to
biological cells, these components should be easily mass-produced,
initially as identical copies of each other, and only acquire their
specialized positions and functions by themselves within the system,
once mixed together.
For example, MIT's "amorphous computing" has set the stage for a
myriad of micro-processors containing the same instructions to
self-organize without exact blueprint map or functional reliability,
unlike traditional VLSI (e.g., Abelson et al. 1999, Nagpal 2002).
Such self-assembling components can also represent mobile sensors
and actuators in complex self-managing networks (Beal &
Bachrach 2006). In software applications (servers, security, etc.),
a swarm of small-footprint software agents can diversify and
self-deploy to achieve a desired level of service (Hofmeyr &
Forrest 2000). In robotics, too, whether articulated parts of
reconfigurable devices (Lipson & Pollack 2000), or mobile
formations of mini-robots (Christensen et al. 2007), there is
also great demand for controllable complex morphologies.
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Selected publications
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Doursat, R. (2006b)
The growing canvas of biological development: Multiscale
pattern generation on an expanding lattice of gene regulatory networks.
1809.
Doursat, R. (2008b)
Organically grown architectures: Creating decentralized, autonomous
systems by embryomorphic engineering.
In , R. P. Würtz, ed., pp. 167-200, Springer-Verlag.
Doursat, R. (2009b)
Facilitating evolutionary innovation by developmental modularity and variability.
Generative & Developmental Systems Workshop
(), at
18th Genetic and Evolutionary Computation Conference
(),
July 8-12, 2009, Montreal, Canada.
Doursat, R., Sayama, H. & Michel, O., eds. (2010)
Morphogenetic Engineering: Toward Programmable Complex Systems,
NECSI "Studies on Complexity" Series, Springer-Verlag.
In Preparation.
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References
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Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, Jr., T.,
Nagpal, R., Rauch, E., Sussman, G. & Weiss, R. (1999)
Amorphous Computing.
MIT Artificial Intelligence Laboratory memo no. 1665, Aug. 1999.
Beal, J. & Bachrach, J. (2006)
Infrastructure for engineered emergence on sensor/actuator networks.
IEEE Intelligent Systems, 21(2): 10-19.
Carroll, S. B., Grenier, J. K. & Weatherbee, S. D. (2001)
From DNA to Diversity.
Blackwell Scientific, Malden, MA.
Christensen A., O'Grady, R. & Dorigo, M. (2007)
Morphology control in a self-assembling multi-robot system.
IEEE Robotics & Automation Magazine, 14(4): 18-25.
Coen, E. (2000)
The Art of Genes.
Oxford University Press.
Hofmeyr, S. A. & Forrest, S. (2000)
Architecture for an artificial immune system.
Evolutionary Computation, 8(4): 443-473.
Lipson, H. & Pollack, J. B. (2000)
Automatic design and manufacture of robotic lifeforms.
Nature, 406: 974-978.
Nagpal, R. (2002)
Programmable self-assembly using biologically-inspired multi-agent control.
1st International Conference on Autonomous Agents,
July 15-19, Bologna, Italy.
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