Monday, March 31, 2025
Lecture Notes Chapter 5: Life is Stranger than Fiction
Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology?
Labels: #ArtificialLife, #biocomplexity, #biology, #genetics, #genomics
Monday, March 24, 2025
Links for "Computation in Cellular Automata" lecture
Conway's Game of Life
Game of Life Demo
Game of Life Applet
3-D Game of Life
Recursive Universe of Game of Life
Game of Life Reveals Long-Sought Repeating Patterns
Turing Machine Implemented in Game of Life
Rule 110
Rule 110 and Universal Computation
Computation Theory of Cellular Automata
A Computational Mechanics Reading List by Cosma Shalizi
Game of Life Demo
Game of Life Applet
3-D Game of Life
Recursive Universe of Game of Life
Game of Life Reveals Long-Sought Repeating Patterns
Rule 110 and Universal Computation
Computation Theory of Cellular Automata
A Computational Mechanics Reading List by Cosma Shalizi
Labels: #cellularAutomata, #Computation, #DensityTask, #emergentComputation, #GameofLife, #UniversalComputation, Class Links
Lecture Notes (Chapter 4): Self-organization and emergent complex behavior
4. Self-Organization and Emergent Complex Behavior
Labels: #DynamicalSystems, #evolvability, #geneRegulation, #robustness, #self-organization
Monday, March 17, 2025
Links for "Automata Networks, Self-Organization and Criticality Hypothesis" lecture
Cybernetic Beginnings of Boolean Networks via Warren McCulloch and Stuart Kauffman
Random Boolean Networks Tutorial by Carlos Gershenson
Random Boolean Networks Demo by Wolfram
BooleSim by Mathias Bock
Discrete Dynamics Lab
Booleannet tool for simulating biological regulatory networks in a boolean formalism by Istvan Albert.
CANA Control and Redundancy in Boolean Networks by Rion Correia and CASCI.
Muramator Robot
Spontaneous Order and Self Organization @ Scholarpedia
Boolean networks beyond Systems Biology: Musical Morphogenesis
Devin Acker's Elementary CA Demo
Cellular Automata Rules
Cellab
New Kind of Science Applets
Wolfram CA Demos
Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet
Random Boolean Networks Tutorial by Carlos Gershenson
Random Boolean Networks Demo by Wolfram
BooleSim by Mathias Bock
Discrete Dynamics Lab
Booleannet tool for simulating biological regulatory networks in a boolean formalism by Istvan Albert.
CANA Control and Redundancy in Boolean Networks by Rion Correia and CASCI.
Muramator Robot
Spontaneous Order and Self Organization @ Scholarpedia
Boolean NK Networks from the Wolfram Demonstrations Project by Garrett Neske
Boolean networks beyond Systems Biology: Musical Morphogenesis
Devin Acker's Elementary CA Demo
Cellular Automata Rules
Cellab
New Kind of Science Applets
Wolfram CA Demos
Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet
Labels: #BooleanNetworks, #cellularAutomata, #edgeOfChaos, #self-organization, Class Links
Tuesday, February 25, 2025
Companion Links for chaos and logistic map lecture
Logist Map Plots and Analysis by Dirk Brockman for Complexity Explorer
Wolfram demo for the Logistic map and detailed study.
Java Code for Time Series of Logistic Map
GDScript Code for Logistic Map
Andrew Clem ~ Chaos theory contains a very nice explanation of the logistic map and the white bands of periodic behavior inside the chaotic range. Try r=3.84 in the demo used in class, to see a cycle of 3 arise.
See also The birth of period 3, revisited.
Applications of constrained chaos:
Two-dimensional constrained chaos and industrial revolution cycles: "Since the 1760s, at least three industrial revolutions have occurred. To explain this phenomenon, we introduce two-dimensional (2D) constrained chaos. Using a model of innovation dynamics, we show that an industrial-revolution-like technology burst, driven by investment/saving motives for R&D activities, recurs about every one hundred years if the monopolistic use of a new technology lasts about 8 y." Full paper @PNAS.
Non-equilibrium early-warning signals for critical transitions in ecological systems. "We employ landscape-flux theory from nonequilibrium statistical mechanics as a general framework to quantify the global stability of ecological systems and provide warning signals for critical transitions." Full paper @ PNAS.
Wolfram demo for the Logistic map and detailed study.
Java Code for Time Series of Logistic Map
GDScript Code for Logistic Map
Andrew Clem ~ Chaos theory contains a very nice explanation of the logistic map and the white bands of periodic behavior inside the chaotic range. Try r=3.84 in the demo used in class, to see a cycle of 3 arise.
See also The birth of period 3, revisited.
Applications of constrained chaos:
Two-dimensional constrained chaos and industrial revolution cycles: "Since the 1760s, at least three industrial revolutions have occurred. To explain this phenomenon, we introduce two-dimensional (2D) constrained chaos. Using a model of innovation dynamics, we show that an industrial-revolution-like technology burst, driven by investment/saving motives for R&D activities, recurs about every one hundred years if the monopolistic use of a new technology lasts about 8 y." Full paper @PNAS.
Non-equilibrium early-warning signals for critical transitions in ecological systems. "We employ landscape-flux theory from nonequilibrium statistical mechanics as a general framework to quantify the global stability of ecological systems and provide warning signals for critical transitions." Full paper @ PNAS.
Labels: #chaos, #logisticMap
Monday, February 24, 2025
Companion links for "Dynamical Systems and Attractor Behavior" lecture
Gravitational Pendulum
The Icosystem Game
Turing Reaction-Diffusion Model of Morphogenesis by Kele W. Cable: a demo by Chris Jennings .
Graphics Research on Reaction-Diffusion
synthetic texture using reaction-diffusion
Reaction-Diffusion in gene expression of digit determination (in mouse)
Validation of predicted patternsin Turing diffusion (in abiological droplets)
Revising the Turing model with biological evidence (in zebrafish)
Turing-type polyamide membranes for water purification
Expanding theoretical models (ABM and others)
Reaction-Diffusion in various areas.
3-Body Gravitational Problem 3-Body Problem in JavaScript
Lorenz Attractor Demo
Wolfram Projects Demo
Plotting Edward Lorenz's 1963 "Deterministic Nonperiodic Flow" in a 3-dimensional space using mplot3d.
Sensitive dependence on initial conditions in the Lorenz Attractor (Python code). Wolfram Sensitivity To Initial Conditions Demo.
Turing Reaction-Diffusion Model of Morphogenesis by Kele W. Cable: a demo by Chris Jennings .
Graphics Research on Reaction-Diffusion
synthetic texture using reaction-diffusion
Reaction-Diffusion in gene expression of digit determination (in mouse)
Validation of predicted patternsin Turing diffusion (in abiological droplets)
Revising the Turing model with biological evidence (in zebrafish)
Turing-type polyamide membranes for water purification
Expanding theoretical models (ABM and others)
Reaction-Diffusion in various areas.
3-Body Gravitational Problem 3-Body Problem in JavaScript
Lorenz Attractor Demo
Wolfram Projects Demo
Plotting Edward Lorenz's 1963 "Deterministic Nonperiodic Flow" in a 3-dimensional space using mplot3d.
Sensitive dependence on initial conditions in the Lorenz Attractor (Python code). Wolfram Sensitivity To Initial Conditions Demo.
Labels: #Attractors, #chaos, #DynamicalSystems, #Dynamics, #ReactionDiffusion, #Turing
Monday, February 17, 2025
Companion links for Self-Similarity and L-Systems Lecture
Fractals
L-Systems
Evolutionary Robots
3D Genbots using L-systems
The GOLEM Project.
See also the research pages pages of Karl Sims, Jordan Pollack, Hod Lipson, Josh Bongard, and Dario Floreano.
- The Koch Curve Fractal, and a generator.
- The Koch Snowflake, and a demo and another.
L-Systems
- A good description and demos by Chris Jennings
- Source Code from Gary Flake's Computational Beauty of Nature Book
- Generate an L-System. An alternative generator, and Another HTML Generator.
- Code for a L-System Explorer
- The Algorithmic Beauty of Plants
- Self-similar syncopations: Fibonacci, L-systems, limericks and ragtime.
- Musical L-Systems by Stelios Manousakis and the Symbolic Composer
3D Genbots using L-systems
The GOLEM Project.
See also the research pages pages of Karl Sims, Jordan Pollack, Hod Lipson, Josh Bongard, and Dario Floreano.
Labels: #development, #fractals, #Lsystems, #morphogenesis, Class Links
Lecture notes (Chapter 3): Modeling the World and Systems Approach to Life
Modeling the World and Systems Approach to Life. Chapter 3 of lecture notes now online.
Labels: #artificallife, #computationalBiology, #Hertz, #information, #modeling, #SystemsBiology, #SystemsScience
Friday, February 14, 2025
T cell specificity from partial information
An example of using Information Theory to predict T-Cell Specificity in the immune systems. Full paper @ PNAS.
Labels: #immunesystem, #infomation
Thursday, February 13, 2025
LLMs and World Models
Loved this piece by Melanie Mitchell: "I’d guess that it’s actually our human limitations [...] and complex environments that require us to form more abstract and generalizable internal models." Her thinking is very much in line with Pattee's and Rosen's concept of internal models, especially the former's notion of "selective loss of detail.
Labels: #AI, #InternalModels, #LLM, #modeling
Monday, February 10, 2025
Links for "Modeling Principles of Organization" lecture
Pi the Movie
Fibonacci Sequence
D'Arcy Thompson
- Fibonacci numbers in Nature. The Romanesco Vegetable.
- Fibonacci Spiral Demo. Another Demo.
- Fibonacci Music
The magic of Fibonacci numbers by Arthur Benjamin
Peter Hilton (1923-2010) discusses intriguing number tricks that can be explained by analysing the properties of Fibonacci numbers and the related Lucas numbers. The explanations themselves benefit from further explanations which, in their turn, lead to further discoveries. Recorded at Imperial College London during the 1996 London Mathematical Society Popular Lecture series.
D'Arcy Thompson
- In retrospect: On Growth and Form by Phillip Ball.
- D'Arcy Thompson's Affine Fish Transformations @ Wolfram
- S.J. Gould. [1971] "D'Arcy Thompson and the Science of Form". New Literary History, 2 (2): 229-258
- W. Arthur [2006]. "D'Arcy Thompson and the theory of transformations".Nature Reviews Genetics 7, 401-406.
- Geometry of Growth and Form: Commentary on D'Arcy Thompson
- Java applet for shell sketching
Patterns of Life – D’Arcy Thompson, Structuralism and the Shape of Life
Treasures of the Library 5. D'Arcy Thompson, On growth and form
BLOOMS: Strobe Animated Sculptures Invented by John Edmark from Charlie Nordstrom on Vimeo. "This series of 3D printed sculptures was designed in such a way that the appendages match Fibonacci's Sequence, a mathematical sequence that manifests naturally in objects like sunflowers and pinecones. When the sculptures are spun at just the right frequency under a strobe light, a rather magical effect occurs: the sculptures seem to be animated or alive!"
Labels: #DArcyThompson, #Fibonacci, #modeling, #morphogenesis, #recursion, ClassLinks
Sunday, February 09, 2025
Lecture Notes (Chapter 2): The Logical Mechanisms of Life
The Logical Mechanisms of Life
Labels: #ArtificialLife, #BiologicalTheory, #ComplexSystems, #GeneralSystems, #SystemsScience, #Theory
Tuesday, January 28, 2025
Self-Assembling Wires
The video shown in class of self-assembly of wires made of metal bearings.
Labels: #self-assembly, #self-organization
Monday, January 27, 2025
Links for Information Lecture 2
Information Basics
Information Theory Tutorial
Letter frequency in English
Word and Letter Frequency in English
Entropy of English
Text Mechanic - Text Manipulation Tools
1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com
Information Theory Tutorial
Letter frequency in English
Word and Letter Frequency in English
Entropy of English
Text Mechanic - Text Manipulation Tools
1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com
Claude Shannon Demonstrating Theseus
Labels: #entropy, #information, #life
Wednesday, January 22, 2025
Mathematicians discover new class of shape seen throughout nature
‘Soft cells’ — shapes with rounded corners and pointed tips that fit together on a plane — feature in onions, molluscs and more. Full news article by Philip Glass at Nature.
Labels: #Mathematics, #Morphology
Lecture notes (chapter 1): What is Life?
Welcome to Life-Inspired, ISE483/SSIE583 Spring 2025 Class. On this blog you will see many types of posts related to the class, from links to multimedia materials used in class, to breaking research on related topics. The updated first chapter of the course's lecture notes is now available:
ISE483/SSIE583: What is Life?
You can also listen to the AI-produced podcast of this chapter via Google NoteBookLM. Note, the AI-podcast does not substitute the lecture notes at all! it brings up many connections not really in the argument, it is provided for fun only.
You can also listen to the AI-produced podcast of this chapter via Google NoteBookLM. Note, the AI-podcast does not substitute the lecture notes at all! it brings up many connections not really in the argument, it is provided for fun only.
Labels: #artificallife, #bioinspiredcomputing, #ComplexSystems, #evolutionarysystems, #life
Wednesday, May 08, 2024
How DNA encodes the start of transcription
Very cool use of machine learning to infer more precise rules of RNA transcription from DNA, including, strength, local and long-rage instructions: "The rules rely on three types of sequence patterns: motifs, initiators, and trinucleotides. The nine motifs are the main drivers of transcription initiation signals and can have short- or long-distance effects. The 11 initiators fine-tune transcription initiation signals but only have local effects. The 32 trinucleotides (representing all three-nucleotide combinations of A, C, G, and T) account for the remaining sequence dependencies not captured by motifs and initiators and have mostly local effects." Full news article and the original paper @ Science.
Labels: #code, #dna, #RNA, #TuringTape
Friday, April 19, 2024
Complexity Thoughts
Complexity Thoughts is a wonderful digest of research in complex systems, theoretical bioology, and biomedical complexity, annotated by Manlio Dedomenico.
Labels: #complexity
Monday, April 01, 2024
Your Fancy-Pants Brain
"What vindicates the complex-systems people, as I see it, is the recognition of “emergent behaviors,” unexpected phenomena that arise from seemingly simple interactions." James Gleick, Full interview by Daniel Drake at New York Review of Books.
Labels: #ComplexSystems, #emergence, #reductionism
Wednesday, March 20, 2024
Modeling and managing behavior change in groups: A Boolean network method
"Social influence processes can induce desired or undesired behavior change in individual members of a group. Empirical modeling of group processes and the design of network-based interventions meant to promote desired behavior change is somewhat limited be-cause the models often assume that the social influence is assimilative only and that the networks are not fully connected. We introduce a Boolean network method that addresses these two limitations. In line with dynamical systems principles, temporal changes in group members’ behavior are modeled as a Boolean network that also allows for application of control theory design of group management strategies that might direct the groups to-wards desired behavior". Full paper @ Advances.in/psychology.
Labels: #BooleanNetworks, #control, #SocialModels
Saturday, February 17, 2024
Toward first artificial plant genome
Researchers have crafted synthetic genomes for several types of bacteria, and an 18-year-long project to do the same for brewer’s yeast is close to completion. Now, a group in China has tackled a multicellular organism, synthesizing part of the genome of a type of moss.Full news article at Science.
Labels: #artificialGenome, #genomics, #SyntheticBiology
Friday, February 02, 2024
Diversity of information pathways drives sparsity in real-world networks
"What if the same physics that governs quantum particles could also explain the peculiar patterns observed in protein-protein interactions, in complex brains, in social relationships, in the Internet infrastructure or the intricate web of air traffic routes? This is not science fiction: it is a mathematical framework, based on thermodynamics and information theory, that has been used for decades to describe entanglement in quantum systems." See an explanation in the great Complexity Thoughts newsletter and the full paper at Nature Physics.
Labels: #ComplexSystems, #information, #thermodynamics
Monday, January 29, 2024
viruslike entities found in human gut microbes
"As they collect and analyze massive amounts of genetic sequences from plants, animals, and microbes, biologists keep encountering surprises, including some that may challenge the very definition of life. The latest, reported this week in a preprint, is a new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. " Full News Report @ "Science"
Sunday, September 10, 2023
Genomic Complexity or Variation in Drastic Fitness Changes
I am fascinated by the recent evidence showing that Polyploidy may grant evolutionary advantages in the presence of drastic fitness changes (e.g. cataclysms). One option is that extra chromosomes may increase connectivity of gene regulatory networks--- fascinating work from van de Peer on that note.
The results remind me of computational experiments we did a long time ago with RNA Editing, where we experimented with drastic fitness changes (simulated cataclysms) and emergence of memory. RNA Editing, we started arguing long ago, also adds additional regulatory variety and proves advantageous in drastic fitness changes---though RNA editing works by adding more variants, not greater number of regulatory possibilities (network connectivity) as it is hypothesized for polyploidy. Maybe this explains why the latter is maladaptive in stable fitness landscapes, whereas RNA Editing often isn't?
Labels: #dna, #evolution, #EvolutionarySystems #Polyploidy #Fitness #GenomeComplexity #Gemome, #GenomicComplexity
Tuesday, April 18, 2023
Multilevel cultural evolution: From new theory to practical applications
Evolutionary science has led to many practical applications of genetic evolution but few practical uses of cultural evolution. This is because the entire study of evolution was gene centric for most of the 20th century, relegating the study and application of human cultural change to other disciplines. The formal study of human cultural evolution began in the 1970s and has matured to the point of deriving practical applications. We provide an overview of these developments and examples for the topic areas of complex systems science and engineering, economics and business, mental health and well-being, and global change efforts. Full article: Wilson, David Sloan, et al. "Multilevel cultural evolution: From new theory to practical applications." Proceedings of the National Academy of Sciences 120.16 (2023): e2218222120.
Labels: #complexity, #evolution, #MUltilevelSelection
Evolutionary Advantages of RNA Editing
RNA editing is hypothesized to facilitate adaptive evolution via flexibly diversifying the proteome temporally or spatially. However, direct experimental evidence is lacking. This study unveils the functional importance of conserved missense adenosine-to-inosine (A-to-I) RNA editing (CME) sites in Fusarium graminearum and provides convincing experimental evidence for the adaptive advantages of two CME sites. The first CME site drives the CME5 gene gaining a new important function in ascus and ascospore formation during evolution. Having an editable A at this site is fitter than an uneditable A or a genomically encoded G. The second CME site in the CME11 gene confers a “heterozygote advantage” during ascosporogenesis, meaning that concurrently expressing both edited and unedited versions is more advantageous than either. Full article: Xin, Kaiyun, et al. "Experimental evidence for the functional importance and adaptive advantage of A-to-I RNA editing in fungi." Proceedings of the National Academy of Sciences 120.12 (2023): e2219029120.
Labels: #adaptation, #evolution, #RNA, #RNAEditing
Friday, March 03, 2023
Organoid intelligence
A new take on Ai, is "Wet" AI using organoids and other sythetic biology methods. "We anticipate OI-based biocomputing systems to allow faster decision-making, continuous learning during tasks, and greater energy and data efficiency. Furthermore, the development of “intelligence-in-a-dish” could help elucidate the pathophysiology of devastating developmental and degenerative diseases (such as dementia), potentially aiding the identification of novel therapeutic approaches to address major global unmet needs." Full article @ Frontiers in Science. Thank you Xuanchi Li for the article.
Labels: #AI, #Brain, #organoids, #SyntheticBiology
Thursday, March 02, 2023
Lane formation in Crowd Dynamics
"Laning is a paradigmatic example of spontaneous organization in active two-component flows that has been observed in diverse contexts, including pedestrian traffic, driven colloids, complex plasmas, and molecular transport. We introduce a kinetic theory that elucidates the physical origins of laning and quantifies the propensity for lane nucleation in a given physical system. Our theory is valid in the low-density regime, and it makes different predictions about situations in which lanes may form that are not parallel with the direction of flow. We report on experiments with human crowds that verify two notable consequences of this phenomenon: tilting lanes under broken chiral symmetry and lane nucleation along elliptic, parabolic, and hyperbolic curves in the presence of sources or sinks." Full article @ Science.
Labels: #Crowddynamics, #Crowds, #self-organization
Wednesday, February 08, 2023
Ants Revisit the Shortest Path Problem
We propose a biologically plausible model, based on a variant of the reinforced random walk on a graph, which explains this observation and suggests surprising algorithms for the shortest path problem and its variants. Full paper @ PNAS.
Labels: #ants, #optimization, #ShortestPaths
Thursday, April 07, 2022
How Cells Conquer Mazes
"Researchers are beginning to understand more about how migrating cells navigate through the body." Full article @ Quanta Magazine.
Labels: #CellBiology, #Dynamics, #Movement, #Pathfinding
Monday, March 14, 2022
Engineered Biological Switches
Scientists created DNA nanotube rails that branch in multiple directions, with each unique track made up of unique DNA patterns. Protein motors designed to recognize these patterns then carry their cargo down the desired tracks. Nanoswitchyards should help scientists better test and understand the real thing inside cells. They may also eventually help researchers steer different drug cargoes to different tissues or engineer novel DNA computers that respond to their environment. In the video, proteins called dyneins have been engineered to glide along DNA tracks. At a branch point, different DNA patterns of the tracks steer dyneins carrying orange fluorescent cargo to the left and dyneins carrying cyan fluorescent compounds to the right.
Labels: #dna, #MolecularComputers, #Switches
Thursday, March 03, 2022
How We Can Make Sense of Chaos
"Dynamical systems can be chaotic and impossible to predict, but mathematicians have discovered tools to help understand them". Full article by David S. Richeson at Quanta Magazine.
Labels: #chaos, #DynamicalSystems
Monday, January 18, 2021
3D underwater collective behaviors in a fish-inspired robot swarm
"most underwater robot collectives rely on centralized, above-water, explicit communication and, as a result, exhibit limited coordination complexity. Here, we demonstrate 3D collective behaviors with a swarm of fish-inspired miniature underwater robots that use only implicit communication mediated through the production and sensing of blue light. We show that complex and dynamic 3D collective behaviors—synchrony, dispersion/aggregation, dynamic circle formation, and search-capture—can be achieved by sensing minimal, noisy impressions of neighbors, without any centralized intervention." Full paper @ Science Robotics.
Labels: #collectivebehavior, #collectiveIntelligence, #Robotics, #Swarms
Tuesday, January 14, 2020
Programmable organisms
Exciting work bridging biology and computing from josh Bongard and Michael Levin, who "present a method that designs completely biological machines from the ground up: computers automatically design new machines in simulation, and the best designs are then built by combining together different biological tissues." Full article @ PNAS.
Labels: #BioRobots, #ProgrammableMatter
