Genetically-Programmable Self-Patterning Swarm Organs

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

This project focuses on exploring and exploiting biological mechanisms of morphogenesis for abstract and technological systems, such as robot swarms. In particular, by transferring and studying these mechanisms in artificial systems, we hope to understand better emergent behaviour within plant developmental.

The collective self-organisation into complex spatial arrangements despite each agent having only local awareness is directly relevant to both biological morphogenesis, and to new paradigms of distributed technology such as robotic swarms and amorphous computing. Two levels of adaptation are either evident or required in these systems: (1) As the whole system changes over time, individual agents find themselves in different local situations and must adapt and adjust their behaviour accordingly, for example dealing with conflict resolution and/or cooperation with neighbours. (2) The swarm must also adapt to the outside world (or the world it is embedded in) in various ways depending on its task – for example, coping with damage, maintaining functionality under changing environmental conditions, or tracking objects. A fundamental challenge in this field is how to design the local control system of each agent, and the Swarm-Organ project will extensively explore a specific approach – namely the use of GRNs (gene regulatory networks) – as a potentially powerful control method for these systems. By focusing on GRNs we will develop a theoretical framework about distributed adaptive control, which will be equally informative to both natural biological morphogenesis, as well as next generation technologies in robotics and computation.

Parallel to this, we will add fundamental features of plant-like structures to the swarms, and investigate the plasticity and robustness of de novo plant organ formation (in silico, in robots and in planta).

Publications

10 25 50
 
Description Sorting of Robots--> We have been able to capture cell sorting processes, in which different cell types are able to sort out in distinct tissues when randomly mixed due to their adhesive properties, in swarms of robots. This is very unique, as the robots we use do not have "membranes" as such, they only interact locally through light. Moreover, we were able to show that the robots (kilobots) due to the inherent imperfections of each unit (they are all slightly differerent, they wobble about, they do not communicate prefectly etc) are generating enough "noise" that allows them to discover the best way to organize themselves as a cohort. Thus, our biological inspiration -- in which membranes of cells fluctuate and hence -- served to show that robot swarms can use noise in a constructive way for larger scale patterning.

Morphogenesis in Robot Swarms --> Together with the other partners, we were also able to succesffuly capture the following biological patterning mechanisms in the kilobots: turing patterns, endothelial membranes, embryo engulfment, root growth and lateral root patterning.
Exploitation Route We have provided the community with specialised software, which is being widely used and made available as open-source software.

We also provided proof-of-principle of how complex auto-organizing processes of biological moprhogenesis can be harnessed in an artificial situation, successfully and in a robust manner towards noise.
Sectors Aerospace, Defence and Marine,Digital/Communication/Information Technologies (including Software),Education,Other

URL http://www.swarm-organ.eu
 
Description We have made educational material that can be used in schools, to show how emergent behaviour can result from simple interactions. This was done in the form of "games" that children could play in the schoolyard. It was distributed to Schools in Spain and in the Netherlands.
First Year Of Impact 2015
Sector Other
Impact Types Cultural

 
Description OpenPlant -- Controlling micro-environments for plant root growth.
Amount £4,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2016 
End 06/2017
 
Description OpenPlant Advancing the ability to image single RNA molecules at the cellular level
Amount £4,000 (GBP)
Funding ID Grant BB/ L014130/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2016 
End 01/2017
 
Title Cell Shape Analysis Code 
Description We have made available the mathematical methodology and code to analysis complex cell shapes. This accompanies the paper in which we explain and show case the method. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2018 
Provided To Others? Yes  
Impact Can be used for plant cells, but also for animal cells. Also, can be extended for organelles or even 2D shapes of organisms. 
 
Description OpenPlant Fund for Development of a Low-Cost Micro-Environment Device for Root-Nutrient Interaction 
Organisation University of Cambridge
Department Department of Plant Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Designing a Low-Cost Micro-Environment Device for Root-Nutrient Interaction. Testing root growth in the diverse prototypes.
Collaborator Contribution Helping to engineer the devices.
Impact Multi-disciplinary study, in which biophysics and plant biology meet.
Start Year 2016
 
Description SwarmOrgan Partnership 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution We have developed simulators for swarm robotics, that can specifically use biologically inspired genetic regulatory networks. This has been made available to the open source community, and we also are working on submitting a manuscript on the simulator. We contribute to the understanding of morphogenesis in self-propelling and locally stimulated agents. We have a paper accepted in Current Opinion in Cell Biology, in which we make an analogy between root architecture plasticity and swarm behaviour, linking molecular details to local and global signalling.
Collaborator Contribution They have efficiently employed our strategies for network evolution and patterning studies. We continue to interact on ideas and projects which emerged from this EC grant.
Impact http://arxiv.org/abs/1511.04285 http://jic-csb.github.io/kilombo/
Start Year 2012
 
Title Kilombo: a Kilobot simulator to enable effective research in swarm robotics. 
Description http://arxiv.org/abs/1511.04285 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Research in swarm computing. 
URL http://arxiv.org/abs/1511.04285
 
Description Collective dynamics and self-organization in biological sciences 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Self-organization is pervasive in biology as living organisms are by essence systems that have self-assembled and self-organized in the course of their development. Self-organization refers to the ability of systems made of a large number of independent agents interacting through rather simple and local rules to generate large scale spatio-temporal coherent structures with typical dimensions orders of magnitude larger than those associated with each individual agent.

By bringing together mathematicians and biologists, this workshop provided a broad overview of the various self-organization mechanisms that prevail at the various scales and the mathematical models by which they can be described or even explained. Through this interaction between experts from different disciplines, the workshop made progress towards determination of the key biological mechanisms that enable self-organisation at each scale and across the scales, and towards the derivation of suitable `universal' mathematical models able to describe them across the scales.

The value of this workshop is twofold. For the biologists, it reinforced their link with mathematicians and, by this strengthened relationship, enlarged the range of models that they can use to probe observed biological complexity. For the mathematicians, it broadend the repertoire of case studies with which to confront their methodologies and practice. It suggested new systems where models are still preliminary if not existent and which may require the development of new mathematical frameworks. For the two communities, it offered the opportunity of building trans-disciplinary teams that can easily share knowledge, models and data and apply to major research councils in UK and in Europe for large grant funding.
Year(s) Of Engagement Activity 2018
URL https://www.icms.org.uk/collectivedynamics.php
 
Description Interview with national news (BBC Radio 4) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interview on the legacy of D'Arcy W. Thompsons' showcasing the research of my Lab (Grieneisen) and this ISP in "On Growth and Form", for BBC radio 4 "ScienceStories". Interviewer was Philip Ball, programme name:
The Man Who Found Physics in Shells, Seeds and Bees, 28 Jun 2017.
Year(s) Of Engagement Activity 2017
URL https://www.bbc.co.uk/programmes/b06vy2jd/episodes/downloads
 
Description Paris Biological Physics Community Day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Postgraduate and undergraduate students from mathematics and physics attended this event to understand how they could contribute to biology.
Discussions about the role of physics in biology was discussed, and students were encouraged to network with the invited speakers and ask career questions.
Also, interested general audience also atteneded.
Year(s) Of Engagement Activity 2018
URL http://www.lcqb.upmc.fr/parisyoung/2018/