sunset

A glorious sunset this evening:

18:58 BST

view from a hotel window

I'm visiting Abertay University for a couple of days, to get a grant proposal with some colleagues here finished off.  This evening, taking a break from editing the proposal, here is the view from my hotel window, looking east over the dock by the river Tay:

Julia sets

Here are some beautiful visual explanations:

How to Fold a Julia Fractal : a tale of numbers that like to turn

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nothing for ages, then three come along at once

Any time you are feeling a bit overwhelmed, read this, and calm down :-)

The Week My Husband Left And My House Was Burgled I Secured A Grant To Begin The Project That Became BRCA1

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A conceptual and computational framework ...

Our latest paper, in PLOS Computational Biology, is snappily titled:  A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells.

Our author summary is:

Pluripotent stem cells possess the capacity both to renew themselves indefinitely and to differentiate to any cell type in the body. Thus the ability to direct stem cell differentiation would have immense potential in regenerative medicine. There is a massive amount of biological data relevant to stem cells; here we exploit data relating to stem cell differentiation to help understand cell behaviour and complexity. These cells contain a dynamic, non-equilibrium network of genes regulated in part by transcription factors expressed by the network itself. Here we take an existing theoretical framework, Transcription Factor Branching Processes, which explains how these genetic networks can have critical behaviour, and can tip between low and full expression. We use this theory as the basis for the design and implementation of a computational simulation platform, which we then use to run a variety of simulation experiments, to gain a better understanding how these various transcription factors can combine, interact, and influence each other. The simulation parameters are derived from experimental data relating to the core factors in pluripotent stem cell differentiation. The simulation results determine the critical values of branching process parameters, and how these are modulated by the various interacting transcription factors.

new chapter!

Got a copy of a nice book through the post today

That's because in it is a chapter by my colleagues and me:

Dominic Horsman, Viv Kendon, Susan Stepney, J. P. W. Young.  Abstraction and Representation in Living Organisms: When Does a Biological System Compute?  in Gordana Dodig-Crnkovic, Raffaela Giovagnoli, eds, Representation and Reality in Humans, Other Living Organisms and Intelligent Machines, pp.91-116, Springer, 2017

Abstract:

Even the simplest known living organisms are complex chemical processing systems. But how sophisticated is the behaviour that arises from this? We present a framework in which even bacteria can be identified as capable of representing information in arbitrary signal molecules, to facilitate altering their behaviour to optimise their food supplies, for example. Known as Abstraction/Representation theory (AR theory), this framework makes precise the relationship between physical systems and abstract concepts. Originally developed to answer the question of when a physical system is computing, AR theory naturally extends to the realm of biological systems to bring clarity to questions of computation at the cellular level.

ECAL 2017, Friday

The final day of the European Conference of Artificial Life, in Lyon; actually only half a day, to allow people to travel home.

The keynote presentation today was Sabine Hauert talking on Swarm engineering across scales: From robots to nanomedicine.  She started off with a description of her work on swarms of flocking robots, and how to control their behaviour without GPS absolute position, only short range wifi and a compass heading, and where the fixed-wing flyers have restricted manoeuvrability.  But these are small swarms: 10s of devices.  At the other end of the scale is use of small particles in nanomedicine, where the numbers are more like 10^13, 12 orders of magnitude larger, and the controlability is even less, having to rely mostly on diffusion and similar processes.  Most of the “programming” goes into the design of the “body” of these “brainless” particles, adjusting parameters such as size, shape, charge, material, and surface decoration with molecules that can interact with cell receptors.  Once the nanoparticles have “leaked” out of the bloodstream into the tissue, they might be activated by light or heat.  The aim is to come up with generalisable design guidelines.  One approach to searching the vast design space is to use a game to crowd-source workable designs for different scenarios.

After coffee was the final technical session of the conference.  I went to the Artificial chemistries and models of cellular dynamics 2 session.  In Transparency Of Execution Using Epigenetic Networks we heard about a form of neural network that can modify its topology during execution.  A Dynamic Model of the Phosphate Response System with Synthetic Promoters in Escherichia coli was a quite detailed simulation of a particular pathway.  I missed the last presentation, as I needed to get back and get ready for the closing session, which included some announcements about ISAL and the Artificial Life journal (I plugged the review article section), and then huge thanks to everyone involved in organising and running this splendid conference.

Then is was a picnic lunch, and saying our goodbyes (until next year?), and travelling home, our brains full of lots of wonderful new stuff.

Travel involved a tram to the train station, the express tram to the airport, a lot of waiting around (I had gone a bit early, as I had heard there were delays at passport control at Lyon; I needn’t have bothered, as they didn’t open passport control until just before the flight was scheduled), an easyJet flight to Gatwick, a train to St Pancras, a walk across the road to Kings Cross, another train, then finally a taxi, arriving home at 11pm.  One book read on the way out; another read on the way home.

ECAL 2017, Thursday

Day four of the European Conference of Artificial Life, in Lyon, with a full day of presentations.

Again, the day started with an excellent keynote: Bill Sellers talking on Synthetic palaeontology: Reconstructing Ancient Life using Virtual Robots.  How did dinosaurs walk?  Could they run?  How can we tell when all we have is fossilised bones?  So, the idea is to build a dynamic model in the computer, which can be validated against modern animals like crocodiles and ostriches (although these do have fundamental differences from the original dinosaurs).
Only a feed forward control mechanism is needed in these models. From the dynamic model, it is possible to evolve gaits, and discover how the animals might have moved.  There are constraints that need to be considered, such as bone strength.  This means big dinosaurs probably didn’t run: the bones in their legs would have snapped on impact.  The same technology can be used to investigate the gait of early humans and various hominins, looking at the evolution from a crouched to an upright posture.

After coffee I went to the Morphogenesis session. The talks had a lot of overlap with the Morphogenetic Engineering Workshop on Monday, but added some more detail.

Lunch was organised with special “junior/senior tables” where we oldies got to impart words of wisdom to the up-and-coming generations; or just have a nice chat, actually.

After lunch I went to the session on Applications of ALife, which I was chairing.  Chairing is always a little stressful: you have to listen to the talk in order to have ready a question to ask if no-one else does (but not ask it if there’s a good flow of questions), and also have to timekeep.  The Effects of Environmental Structure on the Evolution of Modularity in a Pattern Classifier was about evolved hierarchical modularity.  Next was EvoMove: Evolutionary-based living musical companion, which I knew something about, since it was an output from the EvoEvo EU project I was involved with (which explains my several previosu trips to Lyon).  The third talk was unfortunetely cancelled, so we had a slightly awkward half-hour break (we don’t move talks around, in case people want to move between sessions).  Finally was Road Detection using Convolutional Neural Networks, spotting the rather ill-defined edges of some narrow roads through countryside.

Then it was off for coffee, followed by the second keynote of the day: Phillippe Faure on Drug addiction and alteration of decision making process.  This was a discussion of a series of complex and subtle experiments on mice and rats, including some that ran for months: how mice balance exploration of their environment with exploitation of resources; how even genetically identical mice have different "personalities"; how their physical and social environment causes individuation; how addiction to eg nicotine also modifies behaviours other than the desire for nicotine, such as favouring immediate reward over uncertainty; and more.  One part I liked was when someone from the audience asked a questions about the difference between reward and punishment: Faure answered about how the mice avoid punishment, but charmingly added “we don’t do those experiments”.

After this was an announcement about next year’s ALife conference in Tokyo.  Then it was the late breaking poster session, accompanied by wine and cheese, which was sufficiently delicious and plentiful that no further meal was needed.  I attended the European Research Council (ERC) grant information session, which introduced me to “Synergy Grants”, which sound ideal for interdisciplinary work (although they do have a success rate of 2%).

ECAL 2017, Wednesday

Day three of the European Conference of Artificial Life, in Lyon, with half a day of presentations, and half a day of excursions.

To start the day we had a keynote presentation by Csaba Pál on the Evolution of complex adaptations.  The emphasis here is that the current state of an evolved system, such as the complex bacterial flagellum, is not necessarily related to how it evolved.  The question is how can a system that needs several complex adaptations, each of which may be individually deleterious, actually evolve?  The answer is ... complicated.  There are many mechanisms, including non-adaptive origins such as neutral mutations, macro-mutations such as gene and chromosome duplications, mutations affecting multiple traits, pre-adaptation / exaptation, noise, dynamic environments, and more.  The four main methodological pillars used to research these issues are population genetics, systems biology, experimental evolution, and comparative genomics.  This great talk was another example of how nothing in biology makes sense except in the light of the phrase “but it’s more complicated than that”.

After coffee I went to the Artificial Chemistries track.  Structural Coupling of a Potts Model Cell examined the coupling between an organism and its environment, and how that affects the  morphological transition network.   Functional grouping analysis of varying reactor types in the Spiky-RBN AChem (my student’s paper) discussed an AChem where the binding properties are emergent properties of the composed molecules.  Time as It Could Be Measured in Artificial Living Systems discussed the simplest possible clocks that might be exploited by simple systems.  Finally, Delving Deeper into Homeostatic Dynamics of Reaction Diffusion Systems with a General Fluid Dynamics and Artificial Chemistry Model looked at a modification to a thermal Gray-Scott reaction-diffusion system that has a more physically plausible source and sink of material.

After lunch we had a choice of excursions: a vineyard, or old Lyon.  I chose the latter.  A bus took us up to the top of the old city, to the Basilica, an amazing building, cool grey stone on the outside, lush decoration on the inside.

Basilica front aspect

Basilica decorated ceiling

Basilica: one of many murals

Then it was back into the bus, and down the hill to the old town: narrow cobbled streets, tall old buildings, gorgeous smells of fresh food; hidden courtyards and towers, and secret passageways ("traboules") between the streets.  Then back on the bus to return to the hotel.

the old reflected in the new, seen through the bus window

The evening saw us all congregate for the conference dinner on the Hermès restaurant boat.  The boat seemed to spend a lot of time turning around.  GPS helped explain the reason: cast off; turn round to go south down the Rhône past the confluence; turn round to go north up the Saône; turn round to go south down the Saône past the confluence; turn round to go north up the Rhône back to the mooring.  Then back to the hotel using the excellent tram system.

ECAL 2017, Tuesday

Day two of the European Conference of Artificial Life, in Lyon, was the start of the conference proper.  The proceedings for the conference are open access.

We started with a fascinating keynote from philosopher Viola Schiaffonati, on Experimenting with computing and in computing: Stretching the traditional notion of experimentation.  As an ex-physicist, currently computer scientist, with a strong interest in computer simulation of biological and other complex systems, I found this a very useful exploration of the uses of simulation.  Physics-like subjects tend to have strong clear theories, and here “simulation” is more of “prediction without needing to run the experiment”, as in a virtual wind-tunnel, say.  Biology-like subjects, on the other hand, have less well-defined theories: they are more models comprising a “nest” of concepts, results and techniques from a range of sources, and simulations are more “does this nest hang together in correspondence with reality?”, or even “what tweaks do I need to make this nest hang together?”  The talk examined these concepts, put them together in an interesting way, and also had lots of useful references (not least to the “nest metaphor” paper which I need to read in detail).

After coffee I went to the Complex Dynamical Systems track.  Locating critical regions by the Relevance Index introduced a new measure useful for spotting systems at, or moving towards the “edge of chaos”.  Criticality as it could be demonstrated how agents who learn a structure that allows them to exhibit critical behaviour can exploit that learning to explore solutions to complex tasks in different environments.  Reservoir computing with a chaotic circuit was a neat demonstration of how even a (relatively) simple device can perform the complex computations of a reservoir computer.  Finally Signatures of criticality in a maximum entropy model of the C. elegans brain during free behaviour looked at potential critical behaviour in the “brain” of a (relatively!) simple biological organism.

smooth evolvable path surrounded by
rugged unevolvable peaks

After lunch I went to the Evolutionary Dynamics track.  Lineage selection leads to evolvability at large population sizes was a very nice talk demonstrating that the far ago ancestor of today’s creatures was not necessarily the fittest at the time: in a large population some groups can scamper up sharp fitness peaks and get stuck, whereas others trudge slowly up a smooth shallow incline of fitness, and survive to be even fitter in the long term. A 4-base model for the Aevol in-silico experimental evolution platform described the move from the classical binary representation to a four-base representation in the Aevol system, allowing degeneracy in the decoding.    MABE (Modular Agent Based Evolver): a framework for digital evolution research described a new modular architecture that should allow in silico evolution experiments to be set up much more straightforwardly.  Finally Gene duplications drive the evolution of complex traits and regulation described a series of experiments to investigate to various facets of gene duplication in Avida: is it the genetic material in order, or just the material, or just the increase in genome size, that’s important?

Then after another coffee break (hydration is very important at these events!) there was the second  keynote of the day: a fine double act from Andreas Wessel-Therhorn and Laurent Pujo-Menjouet speaking on The Illusion of Life, or the history and principles of animation.  They demon-strated the “12 principles of animation” with simple examples and then how they are realised in actual films.  They showed the clip of the death of Bambi’s mother that traumatised generations of children (myself included), showing that the actual death is never shown, despite the fact that many people remember it vividly. (I am not one of those who falsely recall it being depicted: I was traumatised by the fact of the death, not its depiction!) They also demonstrated how some of these animation principles have been used in the design of the Jibo robot’s movements, to give it “the illusion of life”.

The final event of the day was the poster session, including our Tuning Jordan algebra artificial chemistries with probability spawning functions.  I looked at all the posters quickly, but I then had to go off to the ISAL board meeting, where we reviewed the society’s activities, learned lessons from this year’s organisers, and brought next year’s organisers into the fold.

ECAL 2017, Monday

Day one of the European Conference of Artificial Life, in Lyon, was dedicated to Workshops and the Summer School.

All the workshops running in parallel meant a tricky choice.  In the morning I went to the (half day) Morphogenetic Engineering Workshop. First we had three plant-inspired talks: on simulating complex ecosystems to investigate the evolution of diversity; on guiding the growth of a system by being inspired by plant growth mechanisms; on real-time interactive systems for biological investigations, based on game engines.  After the break there were three more talks, on using the NEAT encoding scheme to evolve cellular automata rulesets; an investigation into criticality in gene regulatory networks modelled using Random Boolean Networks; a multi-level model of autopoiesis to investigate self-organisation.  So the conference was off to a great start!

After lunch I gave a talk on Open-Endedness in Simulations at the ISAL Summer School.  My very brief abstract: Open-ended behaviour in simulated systems is one goal of artificial life, yet the term “open-ended” is rarely defined. Here I discuss a recent definition in terms of models and meta-models, its consequences for discovering multi-scale open-endedness in computer simulations, and some suggested ways forward.  The talk was based on findings/rants from four recent-ish papers: Reflecting on Open-Ended Evolution (ECAL 2011), Bio-Reflective Architectures for Evolutionary Innovation (ALife 2016), Defining and Simulating Open-Ended Novelty: Requirements, Guidelines, and Challenges (2016), and Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry (2017).  Later, a colleague said “I heard you talk on this in Cancun, and thought you were mad.  This time, I think I can see what you are getting at.  Maybe next time I will believe you!”  I suspect this might be partly due to me having had 30 minutes for a highly compressed summary last year, and 90 minutes for a more relaxed approach this time.

I then had the opportunity to drop into the final session of the Living Architectures Workshop. The presentation about the HyperCell project was given via skype, and covered a lot of ground, from a design for the flexible, magnetically connecting “cells” that looked wonderful, to large scale applications for “growing” buildings.

The formal part of the day was completed with a fascinating keynote by André Brack,  Honorary Research Director, CNRS, Center for molecular biophysics, Orleans, France.  The topic was on the origin of life, from Miller & Urey’s now over 60-year-old experiment, to today’s explorations of the solar system, and the possibility of life on exoplanets.  Lots of fascinating chemistry, and delightful anecdotes from a life in science (including, how to get your name on a Science paper by saying “add copper chloride”).

Then it was off to dinner with the other Associate Editors of the Artificial Life journal, for strategy and planning discussions.  I’ve been banging on for years about how important good review articles are to any discipline, so I am now responsible for the reviews part of the journal!

view from two hotel windows

The view from my hotel window at Gatwick airport didn't look quite so interestingly techno-noirish in the cold light of dawn.

One of the advantages for staying at this particular airport hotel: I left hotel reception at 6:45, walked to the automated bag drop area, used the machine to check my suitcase, walked up to departures, was processed through security, and was in the departure lounge by 7:00.  I could have had another 15 minutes sleep!  (But there would have probably been longer queues by then.)

Then we spent 45 minutes sitting in the plane at the gate, while they fixed a dodgy-looking seal.  Sitting on the tarmac at Gatwick on my way to an Artificial Life conference is getting to be a tradition.

We landed at Lyon, and I got the express tram to the city centre, then another tram to my hotel.  As I walked up to it I realised I had been there before.  Same strange decor; same helpful friendly staff; same lack of a hotel restaurant because it's Sunday.  The view from this window is a little more typical than this morning's:

The conference starts tomorrow: I'm looking forward to it!

view from a hotel window

At Gatwick Airport, ready to catch an early flight to Lyon tomorrow, where I will be attending the European Conference on Artificial Life.  This is the techno-thriller-like view from my hotel room window: