Thursday, February 26, 2009
Evolution "for the Good of the Group"
"The process known as group selection was once accepted unthinkingly, then was widely discredited; it's time for a more discriminating assessment". Full article by David Sloan Wilson and Edward O. Wilson @ American Scientist
Wednesday, February 25, 2009
Man, machine and in between
"Brain-implantable devices have a promising future. Key safety issues must be resolved, but the ethics of this new technology present few totally new challenges". Full article @ Nature
Links for Lecture 11
Icosystem - The Game: Description
Logist Map Plot
Iteration versus time for the Logistic map
Time Series of 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 applet used in class, to see a cycle of 3 arise.
See also The birth of period 3, revisited.
Discrete Dynamics
Random Boolean Networks Applet
Discrete Dynamics Lab
Discrete Visualizer of Dynamics
Network Workbench. See Discrete Network Dynamics.
Muramator Robot
Logist Map Plot
Iteration versus time for the Logistic map
Time Series of 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 applet used in class, to see a cycle of 3 arise.
See also The birth of period 3, revisited.
Discrete Dynamics
Random Boolean Networks Applet
Discrete Dynamics Lab
Discrete Visualizer of Dynamics
Network Workbench. See Discrete Network Dynamics.
Muramator Robot
Labels: boolean networks, chaos, discrete dynamical systems, logistic map
New Lecture Notes - Chapter 5
Tuesday, February 24, 2009
Gene could allow lab-grown teeth
"Scientists believe they have found a way to grow teeth in the laboratory, a discovery that could put an end to fillings and dentures. The US team from Oregon have located the gene responsible for the growth of enamel, the hard outer layer of teeth which cannot grow back naturally." Full article @ BBC NEWS
Monday, February 23, 2009
Edward N. Lorenz
Edward N. Lorenz, the MIT meteorologist whose efforts to use computers to increase the precision of weather forecasts inadvertently led to the discovery of chaos theory and demonstrated that precise long-range forecasts are impossible, died of cancer [in April of 2008] at his home in Cambridge, Mass. He was 90.
Edward N. Lorenz, 90; scientist developed influential chaos theory - Los Angeles Times
Edward N. Lorenz, 90; scientist developed influential chaos theory - Los Angeles Times
Labels: chaos
Lecture slides for lecture 9 online
Links for lecture 9
Dynamical Systems
Gravitational Pendulum
Turing Reaction-Diffusion Model of Morphogenesis: an applet by Chris Jennings .
3-Body Gravitational Problem
Lorenz Attractor Applet
Lorenz Attractor Space
Explore Trajectories in the Lorenz Attractor
Sensitive dependence on initial conditions in the Lorenz Attractor. Another one.
Gravitational Pendulum
Turing Reaction-Diffusion Model of Morphogenesis: an applet by Chris Jennings .
3-Body Gravitational Problem
Lorenz Attractor Applet
Lorenz Attractor Space
Explore Trajectories in the Lorenz Attractor
Sensitive dependence on initial conditions in the Lorenz Attractor. Another one.
Labels: attractor behavior, dynamical systems
Sunday, February 22, 2009
Y Chromosome's Evolution
"Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior". Full article:
In Chimpanzee DNA, Signs of Y Chromosome's Evolution at the NYTimes Web site.
In Chimpanzee DNA, Signs of Y Chromosome's Evolution at the NYTimes Web site.
Labels: dna, evolution, genetics
MicroRNAs in early patterning
MicroRNAs influence crucial decisions in the patterning of the early vertebrate embryo, reports a study in Nature. The study is the first example of microRNAs regulating a fundamental signaling cascade, the authors say.
Full Story @ The Scientist
Full Story @ The Scientist
Darwinia
Darwinia is a virtual world populated by artificial evolving creatures. "Darwinia has been overrun by a computer virus which has multiplied out of control. Your task is to destroy the Viral Infection and save the Darwinians from extinction".
Labels: Games, simulation
Thursday, February 19, 2009
Slides for Lecture 8 online
Lecture 8 - Fiction, Reality, and Information in Life
Labels: Artificial Life, biology, epigenesis, modeling
Wednesday, February 18, 2009
A Comeback for Lamarckian Evolution?
Sent by Artemy:
"Two new studies show that the effects of a mother's early environment can be passed on to the next generation. The effects of an animal's environment during adolescence can be passed down to future offspring, according to two new studies. If applicable to humans, the research, done on rodents, suggests that the impact of both childhood education and early abuse could span generations. The findings provide support for a 200-year-old theory of evolution that has been largely dismissed: Lamarckian evolution, which states that acquired characteristics can be passed on to offspring." Full story @Technology Review
"Two new studies show that the effects of a mother's early environment can be passed on to the next generation. The effects of an animal's environment during adolescence can be passed down to future offspring, according to two new studies. If applicable to humans, the research, done on rodents, suggests that the impact of both childhood education and early abuse could span generations. The findings provide support for a 200-year-old theory of evolution that has been largely dismissed: Lamarckian evolution, which states that acquired characteristics can be passed on to offspring." Full story @Technology Review
The long and short of RNAs
"The known world of RNA is expanding faster than that of any other cellular building block. The latest additions are types of long and short non-coding RNAs formed by bidirectional transcription and unusual processing. The relationship between DNA, RNA and protein is no longer as simple as we once thought — that specific genomic sequences are transcribed into messenger RNAs, which are then translated into proteins. In recent years, a flurry of studies has reported the existence of a large and growing family of non-protein-coding RNAs (ncRNAs), describing the different mechanisms of their transcription and their role in regulating gene expression." Full article @ Nature
Labels: complexity, gene regulation, RNA
RNA viruses sneak into host DNA
"Endogenous retroviruses, ancient viruses embedded throughout mammalian genomes, might help RNA viruses permanently integrate into the genomes of their hosts [via their functional Reverse Transcriptase]." article @ The Scientist
Public Misunderstanding of Darwin
On the 200th anniversary of Charles Darwin's birthday two myths persist about evolution and natural selection. Michael Shermer @ Scientific American
Monday, February 16, 2009
a Code Beyond Genetics in DNA
"The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself". Full Story: Scientists Say They’ve Found a Code Beyond Genetics in DNA - New York Times
Research Article: Segal et al [2006]. A genomic code for nucleosome positioning. Nature 442, 772-778.
Research Article: Segal et al [2006]. A genomic code for nucleosome positioning. Nature 442, 772-778.
Labels: code, genetics, information
The Genographic Project
Lecture Slides for Lecture 7 Online
Lecture 7 - Genetic Information at Work
Also see the slides for the special presentations:
Renee Barlow: Tom Ray's Evolution, ecology and optimization of digital organisms
Xin Shuai: Chris Adami's Digital genetics: unraveling the genetic basis for evolution
Also see the slides for the special presentations:
Renee Barlow: Tom Ray's Evolution, ecology and optimization of digital organisms
Xin Shuai: Chris Adami's Digital genetics: unraveling the genetic basis for evolution
Labels: genetics, information
Links for lectures 7 and 8
Mitosis and Meiosis, and a comparison.
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
DNA Anatomy
DNA Replication
Transcription and Translation
"To understand the human genome, researchers must spread their wings to all branches of life". Full editorial @ Nature
The paper about ultraconserved DNA which does not seem to be functional...
Frequent lateral gene transfer
Review of The Music of Life: Biology Beyond the Genome by Denis Noble @ Science
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
DNA Anatomy
DNA Replication
Transcription and Translation
"To understand the human genome, researchers must spread their wings to all branches of life". Full editorial @ Nature
The paper about ultraconserved DNA which does not seem to be functional...
Frequent lateral gene transfer
Review of The Music of Life: Biology Beyond the Genome by Denis Noble @ Science
Lecture Notes Chapter 4
Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology? (pdf document)
Labels: Artificial Life, biocomplexity, biology, genetics, genomics
Sunday, February 15, 2009
Bacterial genome found within a fly's
"DNA transfer from bacteria to animals is more common than thought. Researchers have found a surprise hidden in the DNA of a fruitfly: what seems to be the entire genome of a parasitic bacterium called Wolbachia. Smaller bits of the promiscuous parasite's genetic material turned up in worms and wasps, too." Full Sttory @ news@nature.com
Wolbachia bacteria (yellow) within the developing egg of a fruit fly (red).
Labels: bacteria, dna, DNA transfer, information
tierra and avida
10th European Conference on Artificial Life
ECAL2009: 10th European Conference on Artificial Life. September 13-16 2009. Budapest, Hungary
Labels: Artificial Life, conference
Saturday, February 14, 2009
The 10,000 Year Explosion: How Civilization Accelerated Human Evolution
"The normal story we are told is that as rose civilization, so declined evolution. The 10,000 Year Explosion: How Civilization Accelerated Human Evolution, inverts that formula as indicated by the title." Full story @ Gene Expression
One Giant Leap for Robot-Kind
"Cockroach-inspired design could help Mars rovers and other robots traverse sandy terrain". Full story @ ScienceNOW
Labels: biomimetics, robots
Ancient Virus Gave Wasps Their Sting
"Find solves decades-old debate about mysterious toxins". Story @ ScienceNOW
Labels: biology, DNA transfer, genetics
Monday, February 09, 2009
A cool 3D L-system rendering tool
Amazing flame fractals
Thanks to Larry Yeager for pointing these to me: Amazing flame fractals take your breath away | TechRepublic Photo Gallery
Labels: art, fractals, L-systems
Lecture slides for lecture 6 online
Lecture 6 - Self-Similarity and L-Systems
Labels: development, fractals, L-systems, morphogenesis, self-similarity
Sunday, February 08, 2009
links for lecture 6
D'Arcy Wentworth Thompson. Visualizing change in biological organisms.
Java applet for shell sketching
The Koch Curve Fractal
The Koch Snowflake
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, Dario Floreano, Randy Beer, and Rolf Pfeifer.
Java applet for shell sketching
The Koch Curve Fractal
The Koch Snowflake
L-Systems
- A good description by Chris Jennings
- Gary Flake's Applets
- Generate a Tree as an L-System
- L-Systems Explorer
- Another L-System Applet
- The Algorithmic Beauty of Plants
- L-System Figures
- L-Systems and Music
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, Dario Floreano, Randy Beer, and Rolf Pfeifer.
Labels: L-systems, modeling, morphogenesis, recursion
Sacred Science
"Can emergence break the spell of reductionism and put spirituality back into nature?". Full article @ Scientific American
Stuart Kauffman and his book "Reinventing the Sacred"
Labels: cognitive science, Emergence, religion
Life is what you make it
"How's this for creativity? Take Escherichia coli bacteria. Transform them into light-sensitive organisms by fusing a photoreceptor from the cyanobacterium Synechocystis to a protein in the E. coli membrane. Make a film (in both senses) of such bacteria and use them to record an image with a resolution of 100 megapixels per square inch". For more details see the Special Issue on Synthetic Biology @ Nature
The synthetic biology paradigm. Genetic circuits are composed of interacting genes and proteins (blue shapes, top left). The pointed and blunt arrows represent positive and negative regulation, respectively. Synthetic circuits (top right) based on the natural circuit can be constructed from well-characterized components (red and orange shapes) with similar regulatory effects to form similar or simplified circuits. The dynamics of these synthetic replicas can be compared to the natural system as well as to mathematical models. Analysis of natural circuits, synthetic replicas and models together can help us understand mechanisms used by natural systems.
Labels: artificial gene regulation, gene circuits, synthetic bioology, synthetic life
The Self-Organizing Quantum Universe
"A new approach to the decades-old problem of quantum gravity goes back to basics and shows how the building blocks of space and time pull themselves together". Full article @ Scientific American or via the IU Library for reprint.
Thursday, February 05, 2009
Dog gene 'may aid wolf survival
"Wolves have acquired a genetic mutation for dark coat colour through mating with domestic dogs". Full story @ BBC NEWS | Science
Wednesday, February 04, 2009
Lecture notes Chapter 3
Slides for lecture 5
Lecture Slides: From Computation to Modeling Principles of Organization
Steam-powered Turing Machine at Washington University (collective Work)
Steam-powered Turing Machine at Washington University (collective Work)
Labels: computation, information, turing
Snowflakes promise faster chips
"Chips could run faster and be more energy efficient thanks to a process from IBM that copies nature's creation of seashells and snowflakes". Full Story @ BBC NEWS | Technology
Labels: computation, nature
Tuesday, February 03, 2009
Links for Lecture 5
Turing Machine Simulator 1
Turing Machine Simulator 2
Some resources about the Abacus
Demo and Explanation
Another Demo (The Chinese Abacus)
The Abacus in Various Number Systems
The Antikythera Mechanism
Interactive Relighting of the Antikythera Mechanism
Story @ BBC News
The Antikythera Mechanism Research Project
Cool implementation of Babbage's Difference Engine using LEGO! Photos, description of adder and carry propagation logic, mechanical issues, etc. at: http://acarol.woz.org
Pi the Movie
Fibonacci Sequence
Turing Machine Simulator 2
Some resources about the Abacus
Demo and Explanation
Another Demo (The Chinese Abacus)
The Abacus in Various Number Systems
The Antikythera Mechanism
Interactive Relighting of the Antikythera Mechanism
Story @ BBC News
The Antikythera Mechanism Research Project
Cool implementation of Babbage's Difference Engine using LEGO! Photos, description of adder and carry propagation logic, mechanical issues, etc. at: http://acarol.woz.org
Pi the Movie
Fibonacci Sequence
Labels: computation, modeling
Can Bacteria Rescue the Oil Industry?
"Microbes in oil deposits withstand enormous hydrocarbon loads, intense heat, high salt and immense pressure. How can we put them to work for us?" Full article @ The Scientist
Labels: bacteria
Virtual Virus
This Virtual Virus is the first simulation of an entire life form (from LiveScience.com)
Labels: simulation, virus, whole-organism modeling
Notes and slides for lecture 4
The logical Mechanisms of Life: notes and slides now available.
Labels: Artificial Life, computation
Monday, February 02, 2009
Links for lecture 4
The virtual Cell
More on Cells from Wikipedia
Colonial Algae
A Science Primer on Cells
Cell Structure animation
More on Cells from Wikipedia
Colonial Algae
A Science Primer on Cells
Cell Structure animation
Labels: cell, computation
Social Amoeba Seek Kin Association
"Starving "social amoebae" called Dictyostelium discoideum seek the support of "kin" when they form multi-cellular organisms made up of dead stalks and living spores". Full story @ Science Daily
Labels: colony behavior, life
