Systems Biology – Lesson 5

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.

Systems Biology – Lesson 4

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

Digital Microscope!

Thanks to a generous grant from the Southwest King School Retirees’ Association, we were able to purchase a digital microscope and a set of prepared slides.   This equipment will enable us to recover some of the functionality of a lab in a classroom setting, and will extend our capabilities by allowing us to take digital pictures and movies and to conduct extensive analysis of those images.

Here are our first three images taken with the microscope:

1. Daphnia Head – 40x

Daphnia Head

2. Onion Root Tip – 40x

Onion Root Tip - 40x

3. Onion Root Tip (mitosis!)- 100x

Onion Root Tip Mitosis - 100x

Systems Biology – Lesson 3

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 Unit – Lesson 1

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.

Spring Break!

We made it!  Enjoy your hard-earned week off and don’t forget to finish reading your evolution unit articles.  Responses to the readings are due at the beginning of class when you return from break.  In preparation for our final unit, I have reached out to the crytpocurrency community on Twitter to help us add an interesting twist to our study of Systems Biology.  We have already had some amazing individuals and companies step up and make some big donations!  A list of donors will be kept on the Cryptocurrency page of the blog.  If you have a Twitter account, please be sure to follow our donors and send them a huge thank you!

Evolution – Mini-Unit Wrap-Up

To better understand how DNA mutation drives evolution, students worked through the HHMI’s BioInteractive lesson titled Creating Phylogenetic Trees from DNA Sequences.  Students completed the accompanying PDF worksheet prepared by HHMI.

The Evolution mini-lesson concludes on Friday.  Students will have all day in class on Friday to read up to four articles and respond to questions about the articles.  Students must read the first two articles (1- Carsonella ruddii and 2- Dogs First Domesticated in Europe) and thoroughly answer the questions to earn a grade of Developing (equivalent to a C).  Students who read and answer the questions from the third article (3- And the Genomes Keep Shrinking with questions) will earn a grade of Proficient (equivalent to a B).  To earn a grade of Advanced, students must read the fourth article (4- Vitamin C Evolution) and write a one paragraph summary explaining what they learned, what confused them, what they want to learn more about, and how they would obtain the information they want to learn.

Many students elected to take the reading packet in advance in order to complete the reading on Friday.  However, students do have the option of completing the reading over Spring Break and returning the completed work on Monday, April 14.