Complex Systems

A presentation by Nick Bennett introducing complex systems.

Internet Resources

The project GUTS website.

Netlogo download
Here you can download netlogo, a program useful for creating agent based models.

Protein Synthesis
A model about protein synthesis and RNA.

DNA Interactive
Various activities useful for teaching DNA.

Organic Molecules
General background on organic and biomolecules.

Citric Acid Cycle Animation
A helpful animation on the citric acid cycle.

Mercury Vapor
Five experiments showing the danger of elemental mercury.

Miller-Urey Experiment
Stanley Miller's paper describing the apparatus and results of the Miller-Urey experiment.

Gas Law Program
A gas law applet with a number of adjustable variables and graphs.

Thermodynamic Equilibrium
Temperature balancing experiments.

SFI bulletin
The 2006 SFI bulletin, with an article on the beginning of life.

Visual Molecular Dynamics Program (VMD)
From this website, you can download the Visual Molecular Dynamics program used by Dr. Zan Luthey-Schulten at UIUC. In the outreach area are links to tutorials. After clicking on the VMD Molecular Graphics Viewer link, you can download the free software as well as seeing the gallery of work done by scientists using the visualization tool.

This freeware program is a slightly more user friendly version of the VMD program.

Metabolic Case Study for Students
This clicker case introduces students to a rare genetic disease in which an enzyme is deficient in a critical metabolic pathway—the first step in aerobic respiration. This case challenges students to make connections between energy production, enzymes, and metabolic diseases. Students are exposed to a real life story that serves as a basis for discussing the uses of energy-rich molecules and the importance of complex metabolic pathways catalyzed by protein enzymes. Overall, students should appreciate the importance of each step in a metabolic pathway and the side effects as well as treatments that can emerge from discovering the underlying enzyme deficiency.

A different Origins website

Research Articles

Origin of Life Research Project
The Origin of Life Research project by University of Glasgow.

A Simpler Origin of Life
By Robert Shapiro, from the Scientific American.

A New Biology for a New Century
An article by Carl R. Woese published by the American Society for Microbiology.

The Origin of Life
This is a general article on the origin of life featured in "The American Scientist" written by James Trefil, Harold J. Morowitz, and Eric Smith.

First Life
An article by Michael Russell featured in "The American Scientist".

Articles from Nigel's research group

Ancient Genes in Contemporary Persistent Microbial Pathogens
By Vijayasarathy Srinivasan and Harold J. Morowitz.

Energy flow and the organization of life
An article by Harold J. Morowitz and Eric Smith that looks at life from the standpoint of energy and entropy.

The origin of the RNA world: Co-evolution of genes and metabolism
Shelley D. Copley, Eric Smith, and Harold J. Morowitz.

The evolutionary history of Cys-tRNACys formation
This article was mentioned in Zan's talk on July 15th, 2009.

Humbled by the Genome's Mysteries
Stephen Jay Gould's article that was mentioned during Nigel's talk.

Massive Horizontal Gene Transfer in Bdelloid Rotifers
Horizontal Gene Transfer discussed at Nigel's talk.

Darwinism Must Die So That Evolution May Live
An article by Carl Safina about the future of evolution featured in The New York Times.

Great Lakes Sinkholes: A Microbiogeochemical Frontier
Biogeomolecule article about organisms living in the great lakes.

Hydrothermal Vents

Lost City (Wikipedia)
The wikipedia article on the Lost City hydrothermal vent field.

Black Smokers
An informative page on black smoker vents.

Netlogo Applets

These are java applets of netlogo models. You can run them in your browser (as long you have installed a java runtime environment).
Sunflower Biomorphs Applet
Chemical Equilibrium Applet
Bug Hunt Camouflage Applet
Thermal Vent Simulation Applet (Note: Running this model as an applet requires Java 1.6, and a lot of available memory; depending your configuration, you may have better luck downloading the associated .zip file, below, and running the model directly in NetLogo.)
Citric Acid Cycle Exploration Applet
mRNA Learning Model/Game


Below are several models from the standard Netlogo model library. To run these models you must download Netlogo (See above).

Bug Hunt Camouflage.nlogo33.01 KB
SunflowerBiomorphs.nlogo20.84 KB
ChemicalEquilibrium.nlogo17.95 KB
cac.zip14.52 KB
gas_laws.nlogo31.25 KB
EQ.nlogo14.12 KB
vent_chem.zip25.18 KB