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.

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Friday, April 26, 2024

 

links for "Immune System" lecture



Immune System
Immunology movies at Cells Alive!
An Interpretative Introduction to the Immune System. by S. A. Hofmeyr.
Immunology as information processing. by S. Forrest and S. A. Hofmeyr.









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Thursday, April 25, 2024

 

Links for "Self-Reproduction and Open-Ended Evolution" Lecture

Robot Self-replication
Cornell Creative Machines Lab: Self replication
Soft Robotics Evolution


An implementation of Von Neumann's Self_reproducing Automata.







Self-Reproducing Loops: from Langton's to Evoloop. Hiroki Sayama's Website and demos.

Self-reproducing loops

Langton's Loop Applet .






Self-reproducing Xenobots.







autocatalytic networks
Lack of evolvability in self-sustaining autocatalytic networks
Darwinian properties and their trade-offs in autocatalytic RNA reaction networks

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links for Collective Behavior and Swarms lectures



Chemotaxis, Stigmergy, Termites and Ant Clustering and Sorting
Artificial Termites.
Ant-like task allocation and recruitment in cooperative robots
Cells Solving mazes and optimal paths
Self-generated gradients of chemicals and physical tension, cells in the body steer themselves to vital destinations.
Swarm Robotics @ Bristol Robotics Laboratory.
NetLogo





Artificial Ecosystems
Michael Conrad's Work
PolyWorld
Sim Life and Spore (More on Spore).




Collective Behavior
Boids
Boids Demo. Experiment with different interaction ruleson another demo.
Javascript for Boids. Implementing boids in Python.
EPFL Laboratory for Intelligent Systems
A Swarm of One Thousand Robots

Boid -flocking Simulation with python


Flocking with fixed-wing robots at EPFL


Particle Swarm Optimization
Particle Swarm Optimization Paper by Kennedy and Eberhart..
Particle Swarm Optimization Demos.
Particle Swarm Optimization Visualization by Axel Thevenot.
Software Resources for PSO. PySwarm (Python code). Tutorial for coding PSO in Python.
PSO for prediction of protein-ligand interaction

Ant Colony Optimization
Ant Colony Optimization Resources
Ant Colony Optimization Demo


Swarm-bots
Braitenberg (reactive) Vehicles.



Swarm Paintings and a conceptual update (using pheromone fields by Vitorino Ramos).

IdMind. Leonel Moura's robot art including RAP (Robot Action Painter).


Collective Dynamics



Dirk Helbing's Videos and Simulations
Traffic Dynamics in Urban Road Networks and Simulation of Multi-lane traffic. A video with stop-and.go dynamics
Mexican Wave
Simulate Escape Panic. Crowd Turbulence







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Wednesday, April 24, 2024

 

Full Lecture Notes: Evolutionary Systems

Chapter 7 Modeling Evolutionary Systems now available. The entire lecture notes for 2024 also available, including in a pdf booklet.

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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.

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Monday, April 15, 2024

 

Links for "Evolutionary Algorithms" Lectures

Modeling Evolution

Introduction to Genetic Algorithms
Illustrating Evolutionary Computation with Mathematica
Genetic Algorithm Tutorial with Java Code
Genetic Algorithm Walkers
PyGAD - Python Genetic Algorithm and paper with details




Genobots: Generative Representations for Design Automation
The Golem Project
Genetic Programming Resources
Annual "Humies" Awards For Human-Competitive Results Produced By Genetic And Evolutionary Computation
Eureqa models, part of DataRobot: a software tool for detecting equations and hidden mathematical relationships in data. Older version, also at softsea.com.
gplearn: Genetic Programming in Python



Biomorph demo and Python code
Icosystem - The Hunch Engine™




From Artificial Evolution to Artificial Life (1999), Tim Taylor's PhD Dissertation. Check his overview of open-ended evolution.
Evolved Open-Endedness, Not Open-Ended Evolution, By Howard Pattee and Hiroki Sayama


BEACON: Center for the Study of Evolution in Action. biologists, computer scientists, and engineers study evolution as it happens and apply this knowledge to solve real-world problems.

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Lecture Notes: Chapter 6 - Von Neumann and Natural Selection

6. Von Neumann and Natural Selection

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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.

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Monday, March 25, 2024

 

Links for "Genes as Turing Tape" Lecture



Brenner, Sydney. [2012]. "History of Science. The Revolution in the Life Sciences". Science 338 (6113): 1427-8.
Brenner, Sydney. [2012]. "Turing centenary: Life's code script. Nature 482 (7386) (February 22): 461-461.
The virtual Cell
Inside the Cell
Cell Biology at the Biology Project
More on Cells from Wikipedia
The Cell Image Library and highMag
Colonial Algae


Genetics and Genomics

Watson and Crick's Molecular structure of Nucleic Acids 1953 article
Journey into DNA
Cracking the Code of Life (PBS Show)
Explore a stretch of code



Translation and Protein Synthesis
Interactions between the Translation Machinery and Microtubules

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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

Neural Cellular Automata For Art Recreation

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Lecture Notes Chapter 5: Life is Stranger than Fiction

Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology?


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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.

eighteen state-transition graphs of models.

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Monday, March 11, 2024

 

links for "Cellular Automata and Edge of Chaos" lecture

Boolean networks beyond Systems Biology: Musical Morphogenesis


Devin Acker's Elementary CA Demo
Cellular Automata rules lexicon at MCell.
Cellular Automata Rules
Cellab
New Kind of Science Applets
Wolfram CA Demos



Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet

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Monday, February 26, 2024

 

Links for "Boolean Networks and Self-Organization" 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

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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.

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Sunday, February 25, 2024

 

Lecture Notes (Chapter 4): Self-organization and emergent complex behavior

4. Self-Organization and Emergent Complex Behavior

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Monday, February 19, 2024

 

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.



Reaction-Diffusion in Nature

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.


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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.

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Monday, February 12, 2024

 

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.

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Links for "Modeling Principles of Organization" lecture

Pi the Movie

Fibonacci Sequence

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

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!"

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Sunday, February 11, 2024

 

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.

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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.


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Monday, January 29, 2024

 

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

Claude Shannon Demonstrating Theseus

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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"

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Lecture Notes (Chapter 2): The Logical Mechanisms of Life

The Logical Mechanisms of Life

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Sunday, January 21, 2024

 

Lecture notes (chapter 1): What is Life?

Welcome to Life-Inspired, ISE483/SSIE583 Spring 2023 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?

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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? 





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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.

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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.


Image from Christofi, T., Zaravinos, A. RNA editing in the forefront of epitranscriptomics and human health. J Transl Med 17, 319 (2019)

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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.

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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.

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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.

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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.

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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.

Video @ Science

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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.

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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.

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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.

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Friday, October 18, 2019

 

Self-healing, path solving mould

"A yellow organism which looks like fungus but acts like an animal has gone on display at the Paris Zoological Park. The slime mould - Physarum polycephalum - has almost 720 sexes and has been described as one of "nature's mysteries" by scientists. It can heal itself in two minutes if cut in half, and detect and digest food despite not having eyes, a mouth or a stomach." From BBC News.

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