Category Archives: Systems Biology

Biology, Ecosystems, Systems Biology

Systems Biology – Lesson 7

Leave a comment

Our efforts to understand how our campus ecosystem fits within the larger Puget sound ecosystem culminated today.  During the first two class days this week, students worked in groups to create presentations comparing and contrasting the Tyee campus ecosystem with the larger Puget Sound region ecosystem.  Students were tasked with identifying at least one aspect of CHON+Energy cycling absent from our campus that could be added back to make our campus more like the larger Puget Sound region ecosystem.

In the current lesson, students watched George Monbiot’s TED Talk about the concept of “rewilding” to encourage them to think big about how to improve the ecosystem of the Tyee campus.  After watching the talk, students worked individually to complete an evaluation of the project their group proposed the previous day to improve the campus.

Ecosystems, Systems Biology

Consolidation of Crypto Holdings

Leave a comment

In preparation for our lesson integrating the concept of cryptocurrencies into the ecosystems portion of our systems biology unit, I have been researching exchanges for the various eco-themed altcurrencies we have received from many generous donors.  Ideally, there would be one exchange to house all of these currencies, but the reality is quite different.  In an effort to maximize class time and provide students with an opportunity to learn how to execute trades, I have decided to consolidate currencies I have donated (from @dogetutor) on Cryptsy in the form of DogeCoins.  I will discuss with students our options for handling the remaining donated coins.  Options include:

1. Students sign up for additional exchanges to receive the altcurrency

2. Students download the altcurrency wallet on their own computer and send their deposit address

3. I trade our holding(s) for DogeCoins, transfer the DOGE to Cryptsy, and distribute to each student

My purpose in sharing this is to reinforce the importance of transparency.  I have selected DOGE as the common currency because of the low transfer fee, it’s ubiquity on the various exchanges, and the interest students have shown in acquiring that particular currency.  Feedback is welcome and appreciated!

Biology, Ecosystems, Systems Biology

Systems Biology – Lesson 5

Leave a comment

This week, students are collecting data about the ecosystem of the Tyee Campus.  There are a number of bunnies on our school campus, with coloration that suggests they may be recent descendants of pets released into the wild.  I presented students with a scenario and a mission: Find the bunnies!  Students spent most of the first class period canvassing the campus looking for bunnies and taking pictures of the habitat.

The next day, students were introduced to CHON (Carbon, Hydrogen, Oxygen, and Nitrogen) and discussed sources of CHON in an ecosystem.  Students began working in groups to consider how to integrate their basic understanding of CHON into their understanding of the local campus ecosystem.  Some groups began creating PowerPoint presentations, while others devised strategies to create a central repository of pictures in DropBox.  If needed, students continued their field work, taking pictures of the local ecosystem to support their presentations.

For the third day of Lesson 5, we reviewed CHON and students began to conceptualize how to create a presentation with the Tyee bunnies as the central player.  Students received a worksheet with a list of readings to help further their understanding of CHON and energy cycling in an ecosystem.  All students must read one core section, while the additional reading sections are to be read by at least one student in the group and shared with the rest of the group using the jigsaw reading strategy.

Ecosystems, Systems Biology

Systems Biology – Lesson 4

Leave a comment

On the first day of class this week, students took a quiz to demonstrate mastery of the Systems and Networks section of the unit.  Afterward, students worked individually to construct one or more networks from a list of seemingly random biotic and abiotic factors.  The list was actually populated by the names of the various cryptocurrencies students will receive at the end of the unit.

The next day, students shared the strategies they used to construct their networks.  Specifically, we discussed what their edges represented – what was moving through their system.  Many students modeled energy cycling by creating a food web.  Others sought to include the abiotic factors and modeled things like the Earth-Moon-Sun system or the Water Cycle, integrating the biotic factors into that schema.  During work time, students worked in groups of up to 4 students to integrate their individual systems into a larger representation of an ecosystem.  This activity created the foundation for the computer modeling activity in the next lesson.

With a guest speaker scheduled for Friday, we once again are limited to only three days of class this week.  For the third and final lesson of the week, students learned to use formulas to dynamically link individual cells in a Microsoft Excel 2013 spreadsheet.  Students began by making a list of the organisms in their group models.  Next, they assigned quantity values to each organism to represent the amount of each type of organism that must be consumed by a predator of that organism to sustain the predator.  Students shared possible strategies that could be used to estimate those values.  Students then created formulas to relate the organisms.  The relationship formulas enable future modeling predictions based on scenarios that might occur.  For example, we could model what might happen if an invasive species enters an ecosystem and reduces the quantity of one of the organisms in the network.

The sequencing of the Systems Biology unit has been adjusted from the original plan to account for scheduling realities.  As a student teacher at Highline high School, our principal would frequently say, “Monitor and adjust.”  Such insight!  Our updated unit flow will now look something like:

1. Introduction to Systems

2. Ecosystems and Modeling

3. Integration of Economics into Ecosystems

4. Human Body Systems

Biology, Systems Biology

Systems Biology – Lesson 3

Leave a comment

After learning how to define networks in lesson 1, and how to analyze a network in lesson 2, students were tasked with constructing a network in lesson 3.  Students worked in groups of up to four people to construct an economic network, with each student contributing at least 5 nodes and 5 edges.  The ability to understand how networks function, and how to analyze and construct a network will be valuable skills as we move forward in the unit and investigate human body systems, ecosystems, and the integration of the emerging cryptocurrency economy with our study of ecosystems.

Systems Biology

Systems Biology Unit – Lesson 1

2 Comments

During the last two months before summer break, we will spend our time studying the field of Systems Biology.  The Systems Biology Unit will consist of at least four major parts:

  1. Understanding Systems
  2. Human Body Systems
  3. Ecosystems
  4. Modeling of Ecosystems with Eco-Themed Cryptocurrencies

In lesson 1, students were introduced to the overall structure of the unit.  They learned and key vocabulary associated with network analysis, and then applied their learning to define the nodes and edges of familiar systems.  Students worked individually or with partners to define a system, and then examples were shared with the rest of the class.