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Archive for December 6th, 2009

Science & Soul: Cellular Automata


Science News in Brief

Turns out that the Iron Curtain helped isolate Eastern Europe from more than the Western world.  It also blocked the import of alien bird species.  Restrictions on the movement of people and trade in Soviet bloc countries prevented invasive birds being imported, a problem which has plagued much of Western Europe.

There is a difference: An introduced, alien, exotic, non-indigenous, or non-native species is one found outside its native range, having been brought their by humans through deliberate or accidental means.  Invasive species are introduced, but also have a detrimental effect on the environment.

The Intergovernmental Panel on Climate Change (IPCC) released a statement that the emails hacked from scientists’ computers did not contain information which indicated that human created greenhouse gases were not a factor in global warming.

Quirky Quote: “There is an anti-change group. There is an anti-reform group. There is an anti-science group, there is a flat Earth group, if I may say so, over the scientific evidence for climate change.” –Gordon Brown

Researchers have released a study showing that there are large variations in the amount of carbon being absorbed in the North Atlantic: as much as 10%.   They are still doing research to understand what causes these differences.  Currently, the ocean absorbs about half of carbon emissions from human activities.

Apocalypse Scenario: Here’s a nice positive feedback loop for ya: as the climate warms, the ability of liquids to absorb gases decreases (think pop cold vs pop warm), increasing global temperatures, decreasing the ability of the ocean to absorb carbon dioxide…crap.

Cool Creature: Superb Fairywren

Cute Superb Fairywren

The Superb Fairywren, Malurus cyaneus,  is a a small bird found across south-eastern Australia.  The male of the species has a bright blue head, back and tail, with a dark mask, and buff belly.  The female, however are a dull brown colour.  This example of sexual dimorphism is fairly common in the bird world.  The bird is known for its strange mating behavior.  The male wren will pluck yellow flower petals and display them to females.  Although it is socially monogamous, in that they will form fairly regular pairings, but one male will father many chicks with multiple females.  And, he will help raise most, if not all of them.  This causes a rather complex social dynamic.

Feature Story: Cellular Automata

So this is my first post where I talk about what I do as a bioengineer.  People often tell me, “So you mess with genes and stuff, right?”  First, nobody is “messing” with anything.  Second, not really.  I specifically enjoy working with complex ecological systems.  I work to better understand the causes and effects of environmental changes due to natural and human-caused events. Bioengineering allows me to have a holistic look at ecological systems.  Emergent behaviors result from nonlinear interactions between individuals in these ecological systems.  Eventually, I plan to do field research as well as computer modelling to help change the many problems our environment faces.   One of my tools as a bioengineer is cellullar automata.  Have no fear: this is not going to be a trip down molecular biology lane.  Not necessarily anyway.

Networks are built when individuals interact with their local neighborhood, their surroundings.  Thus, range and links are important in a network.  If a system is a complex system with multiple networks, nonlinear interactions among individuals can spontaneously create patterns from an initially random or uniform area. A grid model made up of many individuals represented by cells, or automata (us engineers like to make things complicated sounding), whose possible states are finite and distinct can be updated based on a function which refers to the state of each automata’s neighbors.

Perhaps a good way to explain this is to delve right into an example.  Image a 100 x 100 grid.  This represents a theater.  Each grid space represents a person in the theater.  We want to test the effects of fire on the movie goers.  Let’s say that if 4  people or more around an individual is scared, the middle person is scared.  Otherwise, the cell’s status is normal.  By using a computer program, we can quickly perform multiple iterations of these tests on each of the 10,000 individuals in the test to see if there is any emergent behavior.  Emergent behavior is such that results from nonlinear interactions between autonomous agents in a complex system. That is, it is neither completely random nor completely structured.

So how does this relate to the environment you ask.  Well, I recently completed a project to model ecological succession from bare soil.  Each individual tree species is predisposed to a certain environment.  In turn, each tree affects the environment.  For example, most climax trees are shade tolerant, that is, they grow well in light deficient conditions.  This allows them to grow where there are already a number of pioneer (fast-growing, light-loving) trees.  They in turn create more shade, helping climax trees compete against pioneer trees.  In developing my model, I decided to focus on three main variables which determine plant growth: the soil’s water content, the soil’s pH, and the amount of light in the area.  I also chose the most common trees in an Eastern deciduous forest as my possible states.  To account for the possible variables in the environment, I calculated the amount of trees surrounding a given cell.  The higher the number of trees, the higher the amount of shade, and the less sunlight will reach the trees. I also totaled the number of trees surrounding each cell to calculate water usage.  The more trees there were (as opposed to blank spaces), the less water there was for that area of land.  There are no units for the variables per se, but they can be interpreted as described above.  I then developed a function which would analyze the current state of a cell and compute what the future state of the cell will be.  So, if the current state in the cell is bare soil, then it will either continue to be bare soil or a tree will grow there.  The simulation began with a white field (all blank) as would a piece of land after a disaster leaving bare ground.  In the next time step, pioneer trees came on the scene.  Following this, a few climax trees appeared, and more pioneer trees grew, removing many more of the plots of bare ground.  In the subsequent time steps, more climax trees grew and ultimately dominated the field in the simulation.  By the tenth time step, there was some flux, but most of the trees were of the climax varieties.  There would always be some pioneer trees.  When a tree “died” and resulted in open ground, the first trees to fill the gap would often be pioneer trees, but these are quickly weeded out.  Thus, I used cellular automata to model a biological phenomenon involving emergent behavior.

Secondary Succession: A Cellular Automata Application

Cosmic Perspective

What am I, as a bioengineer, doing with this information?  In my example, I modeled secondary succession, an already understood process.  However, there are other applications.  I know individuals who have used this technique to model forest fires based on forest density.  I have seen the effects of the surroundings on a cell’s (living cell, that is) processes modeled to test new drugs.  The future is truly limitless, but we must understand that we must also ask ourselves whether or not our methods are being applied in such a way to help, rather than harm, the world.  Science is useless without ethics.

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