Ten evening sessions on the mechanisms of pattern formation in Nature, running from January to March 2013 as part of the open studies programme at Edinburgh University.
Course Information
Why do trees look like trees and snowflakes like snowflakes? How do termites build elaborate structures without supervision? What can boiling porridge tell us about clouds? This fully illustrated course explains how patterns in nature can form through self-organisation, using examples and methods from a variety of scientific disciplines. Suitable for anyone who’s ever wondered about the astonishing complexity of nature, you’ll never look at the world in quite the same way again.
Details
- Tutor: Stephan Matthiesen
- Mondays from 14 January 2013 (10 Classes) 18:30 - 20:30
- Turing Room, 15 Buccleuch Place, at the Office for Lifelong Learning, The University of Edinburgh
- Course fee: £85.00/£56.00 conc. - please register at the Office for Lifelong Learning or online through the Course Information Page
- Course code: S217 - Course details
Course contents
14 Jan 2013: Introduction
A tour through patterns in nature, outlining and structuring the topic, and brainstorming: which patterns have students observed in nature?
Presentation: PDF (low resolution, 2.5MB) or PDF (high resolution, 10.9MB)
21 Jan. 2013: Waves and oscillations
We look at waves in the ocean, the atmosphere (cloud patterns!) etc., and why our heart beats.
Presentation: PDF (low resolution, 1.1MB) or PDF (high resolution, 12.2MB)
Videos:
- Waves
- Superposition and interference of circular waves (Youtube): The yellow label at 0:15-0:18 means "Zero order"; you can see a maximum of the amplitude in that direction (zero-order maximum). On both sides of this maximum you can see minima, then (first-order) maxima, then minima again, then higher order maxima and minima.
- Tsunamis
- NOAA: Tsunami forecasts and animation videos (NOAA/Youtube)
- NOAA: 7 December 2012 Honshu tsunami propatation (NOAA/Youtube)
- NOAA: Honshu tsunami event, 11 March 2011: Information and narrated propagation animation (NOAA/Youtube)
- NOAA Tsunami forecasting methods (NOAA/Youtube)
- Oscillating Chemical Reaction (Belousov-Zhabotinsky):
- Oscillating Reaction (Youtube)
- Spatial Patterns in the BZ Reaction (Youtube)
- Spatial Patterns in the BZ Reaction (Youtube)
- Slime Mould Videos:
- Yellow Slime Mould on Wood (Vimeo)
- Slime mold waltz (Youtube): Longer video (9:22 minutes). Some interesting phases to look at: 0:00 amoeba stage (mobile cells); 1:18: aggregation, 1:39: streaming, 2:01: excitation waves; 2:14 "slug" (plasmodium, formed by 1000s of cells), 3:20 formation of fruting bodies (nice one at 3:59)
- Slime mould aggregation from amoeba stage (Youtube)
- Slime mold aggregation, streaming and formation of fruiting body (Youtube)
- Spiral waves in Dictyostelium (Youtube)
- Streaming protoplasmatic strands (Youtube)
- Slime mould solves maze (Youtube)
Additional reading:
- Cartwright, J. H. E., Nakamura, H. (2009). What kind of a wave is Hokusai's Great wave off Kanagawa? Notes and Records of the Royal Society 63 (2), 119-135. URL http://dx.doi.org/10.1098/rsnr.2007.0039
Update:
The Creeping Garden: A documentary about slime moulds and slime mould research is currently in production. The trailer was released on 29. January and is available online: Taster for Creeping Garden (Vimeo).
28 Jan. 2013: Regularity and chaos
Using examples like population cycles or climate fluctuations, we introduce concepts like the logistic equation, bifurcations and attractors.
Presentation: PDF (low resolution, 437kB) or PDF (high resolution, 2.7MB)
Modelling chaos in a spreadsheet:
- Download the Logistic map spreadsheet (you need a spreadsheet programme like MS Excel, OpenOffice or LibreOffice to open it on your computer)
- Vary the parameters in the yellow boxes (r and initial value), see presentation for details
Additional Reading:
- Ensemble forecasting at the MetOffice:
- Current (Canadian) ensemble forecasts from Environment Canada
4 Feb. 2013: Animal swarming and collective behaviour
How fish swarms communicate and how social insects cooperate.
Presentation: PDF (low resolution, 576kB) or PDF (high resolution, 3.7MB)
Videos:
- Social Waves in Honeybees (New Scientist video on Youtube), see also the paper by Kastberger et al (see below, under Additional Reading)
- Swarming behaviour in different animals: Youtube has many videos of swarming and migrating animals, including clips from TV programmes or professional wildlife photographers. They often show impressive scenery and beautiful footage of the animals, but the swarming behaviour isn't always so easy to see. The following videos show collective behaviour quite nicely.
- Sardines
- Starling murmurations at Gretna (Scotland), note the waves at 1:27
- Amazing Starling murmurations
- Falcon attack on Starlings
- Caribou Herd from Helicoptor (from 0:23)
- Duck Stampede
- Boids (Craig Reynold's Website)
- "Finding Nemo" Trailer (Disney/Pixar channel on Youtube): Note the fish swarms at 0:45 and bird flocks at 1:09
- Stop press: Swarming toothbrushes! (Beware of overinterpretation...)
- The clever swarm: This was a series of documentaries and experiments on German TV about swarming behaviour and human crowds, with very interesting footage, but it seems the videos are no longer available online. If you can read German, the programme descriptions give good summaries:
- The clever swarm: a spectacular experiment with 300 volunteers, Quarks&Co, WDR, 10 April 2007
- Mass panic in Mecca: Traffic researchers analyse flow of pilgrims, Quarks&Co, WDR, 10 April 2007
Additional Reading:
- Krause, J., Ruxton, G. D., Krause, S., (2010). Swarm intelligence in animals and humans. Trends in Ecology & Evolution 25 (1), 28-34. URL http://dx.doi.org/10.1016/j.tree.2009.06.016 (behind paywall)
- Katsikopoulos, K. V., King, A. J. (2010). Swarm Intelligence in Animal Groups: When Can a Collective Out-Perform an Expert? PLoS ONE 5 (11), e15505+. URL http://dx.doi.org/10.1371/journal.pone.0015505
- Kastberger, G., Schmelzer, E., & Kranner, I. (2008). Social waves in giant honeybees repel hornets. PLoS ONE, 3(9), e3141. URL http://dx.doi.org/10.1371/journal.pone.0003141
- Ballerini, M., Cabibbo, N., Candelier, R., Cavagna, A., Cisbani, E., & Giardina, I., et al. (2008). Interaction ruling animal collective behavior depends on topological rather than metric distance: Evidence from a field study. Proceedings of the National Academy of Sciences, 105(4), 1232–1237. URL http://dx.doi.org/10.1073/pnas.0711437105
11 Feb. 2013: Spatial patterns
Cracks in mud, paint, soil patterns in Arctic soils, and similar topics.
Presentation: PDF (low resolution, 1.7MB) or PDF (high resolution, 17.3MB)
Videos and material:
- Turing spots (Youtube)
- Tip-splitting in the FithHugh-Nagumo reaction-diffusion system (Youtube)
- Prof. Philip Maini: Turing's theory of developmental pattern formation (Edinburgh University/Youtube); the video of a presentation given at a conference at Edinburgh university. As it is 45 minutes, I will not show it in class.
- Bubbles on a tree (text is in German, but pictures probably speak for themselves)
- Pattern Formation in Nature (Youtube) Many examples from Geology from about 1:00.
- Cut-out model of Arthur's seat (BGS)
Additional literature:
- Rietkerk, Max; van de Koppel, Johan (2008): Regular pattern formation in real ecosystems. Trends in Ecology & Evolution, 23(3), 169–175. DOI: 10.1016/j.tree.2007.10.013.
- Economou, Andrew D; Ohazama, Atsushi; Porntaveetus, Thantrira; Sharpe, Paul T; Kondo, Shigeru; Basson, M Albert; Gritli-Linde, Amel; Cobourne, Martyn T; Green, Jeremy B A (2012): Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate. Nature Genetics, 44(3), 348–351. DOI: 10.1038/ng.1090. (Note that this paper is quite incomprehensible if you're not a developmental biologist; I added it here mainly to show some recent research which indicates the importance of the Turing mechanism).
18 Feb. 2013: Aggregation and growth processes
Crystals, snowflakes, lichen, sunflowers: Find the Fibonacci sequence and the Golden Number in a plastic pineapple!
Presentation: PDF (low resolution, 1.3MB) or PDF (high resolution, 12.8MB)
25 Feb. 2013: Cellular automata and some other topics
How some patterns can be modelled/described by simple discrete models, with applications to the shell of snails.
Presentation: PDF (low resolution, 506kB) or PDF (high resolution, 4.0MB)
Additional Material:
- Mirek's Cellebration: Online Java applet and downloadable Java programme for running cellular automata
4 Mar. 2013: Fractals
Leaves, trees, river systems and other fractal systems.
Presentation: PDF (low resolution, 1.3MB) or PDF (high resolution, 22MB)
11 Mar. 2013: Perception and related topics
(Human) perception of randomness and patterns.
Presentation: PDF (low resolution, 1.0MB) or PDF (high resolution, 7.9MB)
Additional Material:
- Cecilia Burman: Face blindness explained with stones. Original site no longer available, but there is an archived version.
18 Mar. 2013: Summary and Discussions
Patterns, self-organization and emergence.
Presentation: PDF (low resolution, 1.0MB) or PDF (high resolution, 17.8MB)
Additional Material:
- The Wikipedia articles Emergence and Self-organization give reasonable summaries
- Goldstein, Jeffrey (1999), "Emergence as a Construct: History and Issues", Emergence: Complexity and Organization 1 (1): 49–72
25 Mar. 2013: Additional session
This is an additional, optional session where we can recapitulate some of the topics again.
