Sim - Bio 2

A BioQUEST Library VI Module by:

 Elisabeth C. Odum

 Santa Fe Community College

 H. T. Odum

 University of Florida-Gainesville 


About Extend

Investigate Biosphere 2
by Modeling and
Designing Experiments

Problem posing, problem solving, and peer persuasion
 Simulating Biosphere 2
 Biosphere 2 Model
 Results for Biosphere 2 Model

"What If?" Modeling

Room for one more?

Just give us more plants!

How long do we have?

Double, double... toil and trouble?

Is down-sizing the answer?

More Simulation Ideas from the Authors

What if Biosphere 2 was built on forest soil?

What if the floors of Biosphere 2 were sealed?

What if Biosphere 2 utilized outside air?

 Biosphere Processes
 More on the Model
 Publishing/contact information
 Authors' Note

Simulating Biosphere 2

More than 4000 species of plants and animals from nearly 40 nations around the globe were brought into this 3.15 acre, glass-enclosed habitat.

Biosphere 2 is an enormous, glass-enclosed structure built in the mountains near Tucson, Arizona. Eight people lived in this highly engineered complex for two years (1991-1993) as part of a project designed to help us better understand the ecology of the earth, our "Biosphere 1". Biosphere 2 was built as a life scale working model that enabled us to run experiments tracking the interactions among land and water ecosystems and the atmosphere in great detail.

 The Biosphere 2 Center has increased in both size and complexity as shown in this photo taken in February 2000. For a more information, see the website for Biosphere2

Human impact on complex ecosystems and the ways humans can manage these ecosystems can also be studied. The development of self-contained life support systems for living in space stations or traveling long distances is another reason for this experiment. No one knows how big an ecosystem should be to support a human.

During the experiment Biosphere 2 was essentially closed to materials, but open to energy and information exchange. It contained a desert, ocean, rainforest, savanna and marsh, along with an agricultural area and a human habitat, Biosphere 2 is truly a microcosm of planet earth. A huge amount of technology moderated the environment, kept the air circulating as wind inside, varied the temperature and humidity in different areas, and ran the complex computer and communication systems.

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Biosphere 2 Model

Using data from the actual Biosphere 2 experiment, a model of Biosphere 2 was constructed for Sim-Bio 2. You can access this default model (shown below) or assemble it yourself by selecting components from a library of Biosphere variables and then connecting the components. The resulting model can then be run to simulate experimental results.

The icons represent inflows of energy from the sun, photosynthesis by plants producing oxygen and biomass, buildup of dead biomass then consumed by insects and microbes, consumption of plant biomass and oxygen by people, and recycle of carbon dioxide from all consumers both for use by plants and in storage as carbonates in seawater, carbonate-rich soil, and concrete.

Using data from the actual Biosphere 2 experiment, Sim-Bio2 can be used to construct a model and then "run" as a simulation to produce results of interactions over time.

You can see how the different components interact by following the lines leading from the sources (bold black boxes next to icons) to the sinks (light black boxes next to icons). You will notice that except for the sunlight, there is a closed loop between producers and consumption by soils, plant roots, animals, and humans. Each component drives the others, and if one component is changed all the other components change as well.

In the second year of the Biosphere 2 experiment, the Biospherians were experiencing difficulties. Oxygen had to be added and although their diets were supplemented with some stored food, they all lost weight. What was going on?

We can use this model to explore some of the unexpected problems the Biospherians encountered.

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Simulation Results for Biosphere 2 Model:

When you run the model, a graph appears tracing four quantities: Oxygen, Dead biomass, Plants, and Carbon dioxide. Plants and Carbon dioxide are scaled on the left vertical axis, and % Oxygen and % Life support are scaled on the right vertical axis.

Note the relationships between the variables over time:

life support (% of total food and O2 necessary to support humans in Biosphere 2 on right axis)

You can also look at the data for each variable at multiple points in time by searching a table that is located directly below the graph. Compare the results below:

 Day 1  
 Day 1459

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Exploring Biosphere 2

"What If?" Modeling

 Building models is a natural part of the process in most scientific endeavors. Shown here is the small test module which was built as a "proof of concept" model before the much larger Biosphere 2.

What models would you like to build?

Sim-Bio 2 provides "hands on" opportunities for you to learn more about the Biosphere 2 experiment through the design and testing of experimental models. The scenarios below provide different rationales for revising the Biosphere 2 model by changing a single variable. You can work through the following scenarios to practice modeling. Simulation results of each revised model is available for review. You can compare these graphs to the Biosphere 2 simulation graph shown before and evaluate the impacts.

To learn more about what each of the icons stand for, go to More on the Model .

To learn more about how the biosphere works, go to Biosphere Processes


SCENARIO 1: "Room for one more?"

   No entry was allowed at this air lock to the human habitat in Biosphere2 during the experimental period. Once a week, personal visitors could come to "see" and talk to the Biospherians over the phone.

New technical skills are required due to a internal maintenance problem that surfaces on Day 2. A back-up biospherian is sent in on Day 2. What changes do you expect?

What change will need to be made to the model?

How will an extra person affect the level of life support? 


Click to See Results


SCENARIO 2: "Just give us more plants!"

 While many of the plants in the Biosphere 2 habitats were not grown specifically for human consumption, the ripe bananas in the tropical rainforest habitat are likely to have ended up on the table .  

A group of teachers reviewing information on the diminishing % O2 problem found in Biosphere 2 decided to add more plants- twice as many as before- to their models. Will this help?

How could the teachers change the model to add the plants?

Do you expect this will increase the % O2 level?


Click to See Results


SCENARIO 3: "How long do we have?"

 More Biosphere 2 research labs have been built. On the right, you can see one of two spherical "lungs" acting as air handling facilities for the dome.

Considering that emergencies in space might someday require crew transfer to another ship, a group of NASA scientists decided to use the Biosphere 2 model to see how long a rescue ship could support humans if their numbers were suddenly doubled. Even with emergency resources, the humans would begin to expire when the ship's life support level went below 25%.

How would the scientists change the model to simulate the rescue ship with extra astronauts?

How long do you think the crew from the rescue ship will survive?


Click to See Results


SCENARIO 4A: "Double, double... toil and trouble?"

 The view from inside...  

How much extra support will be required if the Biosphere 2 experiment was run for six years?

How would you change the model?

What do you expect to happen?


Click to See Results


SCENARIO 4B: "Is down-sizing the answer?"

If you were able to reduce the number of humans to four, would they still need outside resources to survive a six-year experimental trial?

Building a model to answer this question requires you to make what changes?

Do you think this number of humans will be problematic?


Click to See Results


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More Modeling and Simulation Ideas


Here are three extended scenarios recently suggested by the authors of SimBio2 which involve understanding the relationships between CO2, Carbonates, and O2.


Author Scenario 1: What if Biosphere 2 was built on forest soil?
 Arizona desert surrounding the Biosphere 2.

 The soil used in the construction of Biosphere 2 was heavy organic desert soil. The organic matter in the soil caused more respiration than photosynthesis. This produced excess CO2 which was absorbed by the carbonates. O2 levels dropped as well as the formation of new CO2 incorporated O2 with it.

To simulate the use of forest soil with less organics, simply reduce the organic matter by half. Monitor the O2 and CO2 levels. What is different?

Author Scenario 2: What if the floors of Biosphere 2 were sealed?

  The current Biosphere 2 Center.

 Floors in the Biosphere 2 were sealed with concrete after the first two year experiment. This effectively cut the carbonates in half.

Simulate this by reducing the carbonates to 50% and monitor the CO2 levels.

What do you expect to happen to the O2 levels?

Author Scenario 3: What if Biosphere 2 utilized outside air?

 Since the first experiment, Biosphere 2 has been open to the atmosphere and air has been recirculated in and out by pumping. You can't simulate this since there is no pump icon which can be connected to the O2 and CO2 at this time, but how might you begin to explore the impact of this change on % life support?

How are you using your revised model to explore possible O2 and CO2 changes?

 One of two new air handling stations.

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Biosphere Processes

The basic processes considered in this model are:

1) production

2) consumption

3) recycling of materials

Oxygen, organic matter and carbon dioxide are produced, used, and recycled. Gaseous carbon dioxide exchanges with solid carbonates (limestones etc). The goal of Biosphere 2 was to set up a small similarily balanced system.

Icons represent inflows of energy from the sun, photosynthesis by plants producing oxygen and biomass, buildup of dead biomass then consumed by insects and microbes, consumption of plant biomass and oxygen by people, and recycling of carbon dioxide from all consumers both for use by plants and in storage as carbonates in seawater, carbonate-rich soil, and concrete. As the model shows there is a closed loop between plant producers and consumption by soils, plant roots, animals, humans. Each drives the others, and if one is changed all the others change. In the past the earth has maintained a balanced system.

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More on the Model

Each of the icons in the model is explained.

The mountains of Arizona average about 4000 kilocalories of sunlight falling on a square meter per day. Under the glass and structure of Biosphere 2 the yearly average is about 2000 kilocalories per square meter per day.

Sunlight is essential for plant production of food and oxygen. The more sunlight, the more photosynthesis. In the process of photosynthesis, carbon dioxide, water and sunlight combine to make oxygen and organic biomass.

The plants icon represents all the plant producers in Biosphere 2: algae, grasses, crops, shrubs, trees, phytoplankton in the water, and crops in the agricultural biome. In their green cells they use sunlight and carbon dioxide to produce oxygen and plant biomass. Only a small part of this biomass production (about 10%) is edible food for people; much becomes dead biomass (litter) and is used as food by the small consumers (microbes and ants).

This icon represents all the humans in Biosphere 2 and simply requires you to input a number. The default value is 8 representing the original total of Biospherians in the 1992-1993 experiment.

Oxygen is about 21% of the gases in the air. People cannot be active and comfortable at the altitude of Biosphere 2 (4000 feet) with oxygen less than 16%.

In the Biosphere 2 experiment oxygen started at about 21%; it was used by the microbes and ants as they decomposed the dead biomass in the soil and by people in their respiration. Oxygen was produced by photosynthesis of the plants.

At the end of the second winter oxygen had decreased so much it endangered the life support of the people and more was added from a tank truck. It was the use of oxygen in the consumption of dead organic biomass in the soil that reduced its level, not its use by people.

Carbon dioxide is about 350ppm (parts per million) of the gases in the air. Plants use carbon dioxide in photosynthesis to produce biomass, including food. Microbes, animals and people produce carbon dioxide from their respiration. If the level of carbon dioxide goes down, plant production of food goes down.

Carbonates are chemical compounds found in Biosphere 2 in rocks, concrete and ocean water. Carbonates can absorb or release carbon dioxide depending on its concentration. If there is an excess of carbon dioxide in the air, carbonates will take it in; if carbon dioxide gets low, carbonates will let it out. They act as a buffer to keep the carbon dioxide at moderate levels.

Fallen leaves and lifeless insects are examples of biomass on the ground or in the soil, ready to be decomposed. Soil is a mixture of inorganic particles, like sand and clay, and dead organic biomass from the living parts of the system.

Since the soil put into Biosphere 2 was high in organics (dead biomass), its respiration (by microbes and ants) used more oxygen than was produced by the photosynthesis of the plants. This caused the level of oxygen to decrease to levels dangerous to humans.

Consumers on the ground and in the soil, like soil microbes and ants, use oxygen in the process of consuming this dead biomass for their food. When the soil is rich in organic biomass, the oxygen used in its decomposition can exceed the oxygen being produced by plants. This can reduce the amount of oxygen in the air of an enclosed space like Biosphere 2, making it too low for human survival. In the consumption process, organic biomass and oxygen combine to make carbon dioxide and water.

In the program the combination of food and oxygen needed per person is measured in units of "% of life support". In the second year of Biosphere 2, life support was reduced to 60%. Biospherians were experiencing difficulties. Oxygen was added and their diets were supplemented with some stored food. They all lost weight.

People are also consumers who need adequate oxygen and food to be active in working and thinking. They release carbon dioxide from their consumption processes. If the food and oxygen are below minimum requirements, people lose weight and health. The more people in the chamber, the less food there is for each. Only a part of the green biomass in the agricultural area was edible by humans.

To generate data from your model, you must connect the variables you want to plot to this icon. Note colors for four different plot lines on the left.

Note: Water in Biosphere 2 was abundant and circulated as needed. It was not a changing factor. Therefore, it was made constant in the sim-Bio2 program.

Return to "What If" Modeling

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Produced by the
BioQUEST Curriculum Consortium
This is an association of bio-science educators, who share the belief that science is best learned via the practice of collaborative, open-ended, in-depth scientific inquiry. This philosophy is the motivation for the 3P's approach:


Teaching and learning via

Problem posing, Problem solving,

and peer Persuasion


The BioQUEST Library Volume VI (1999-2000)

Academic Press-San Diego, CA

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Authors' Note:

We acknowledge the encouragement to make this model from John Allen and Mark Nelson, the first managers of Bio2, and the interest of the current managing group from Columbia University.

For more information see the new book from Elsevier entitled Biosphere 2, Research in Progress edited by B. Marino and H.T. Odum.

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3/2/00 es