Category Archives: Systems Biology

Ecology and Systems Biology: Ecosystem Preview

Such talented students at Highline High School!  With several students out of class today preparing for the Homecoming assembly, and short class periods, we reviewed the concept of ecosystem.  We integrated biotic and abiotic factors (two vocabulary words learned yesterday).  We defined an ecosystem as the biotic (living) and abiotic (non-living) factors present in a given space.  We constructed a diagram of a model ecosystem, with students recalling that factors such as plants, animals, birds, insects, water, air, soil, rocks, buildings, mountains, and even the Sun can all be considered factors in an ecosystem.  We characterized the various factors as biotic (for example, plants, animals, insects, and birds) or abiotic (for example, water, air, buildings, rocks, mountains, and the Sun).  We discussed the fact that biotic factors are often found in direct contact with abiotic factors, and both types of factors are necessary for life as we know it.  For example, bacteria are commonly found in all of the abiotic factors listed (except for the Sun!).  We then watched the first 16 minutes of episode 6 of Neil deGrasse Tyson’s Cosmos series.  In the video segment, Dr. Tyson explores the ecosystem of a dew drop.  We were introduced to the tardigrade – an instant class favorite!  Season 1 of Cosmos is currently available streaming on Netflix.

Ecology and Systems Biology: Networks and Factors

We launched our first lesson of Unit 2 (Ecology and Systems Biology) with an introduction to the SQ3R reading strategy.  Details are included in the attached slide deck presented to students before they practiced the SQ3R reading strategy on a reading passage.  The reading introduced students to the vocabulary words of biotic factors (living things) and abiotic factors (things that are not living), and related both types of factors to the study of systems.  Students who were unable to complete the reading in class should finish it as homework and turn it in at the start of class tomorrow morning to receive full credit.

Nature of Science: Self-reflection

What a busy last few weeks!  Instead of a clicker quiz today, students are filling out note cards listing the contents of their lab notebooks.  I will update Illuminate with that information, and students should check their grades this weekend to ensure accuracy.  After filling out the note card, students will have the remainder of the class period to write a self-reflection about how their experience in biology class has been so far this school year.  The reflection should consist of:

  • What you have learned in biology so far
  • How you can use this learning outside of biology
  • What is going well for you in this class
  • What you need to feel safe and successful in class

Students who finish early, or opt to write the reflection over the weekend, may complete any unfinished biology assignments.  Students who are all caught up will have opportunities to earn extra credit.  That includes:

  • Emailing me pictures or video from the milk lab
  • Summarizing the class data set from the milk lab and sharing with the class on Monday
  • Reading and summarizing a Scientific American article from our class library
  • Hanging up Tools Scientists Use posters on the classroom walls

Nature of Science: Tools Scientists Use

In class today, students worked in groups of four to create posters of Tools Scientists Use.  Yesterday, each class came up with a list of tools and wrote the list on their period’s white board.  Today, students in each class made a master list of the tools and then worked with their groups to come up with categories for organizing the tools.  Some of the categories included lab safety equipment, tools used for measurement, and tools that are used for containing liquids.  Other groups organized the tools by area of science, including tools that are used in Integrated Science, Biology, Chemistry, and Physics.  Students then made big, bright posters to present their work.  A selection of the posters will be displayed around the classroom and will help reinforce vocabulary when we prepare for labs.  Also today, students received verbal grade checks and/or reminders that all work must be turned in by Friday for full credit.  Starting next week, the homework policy written in the class syllabus will take effect.

Important Notes: the math worksheet from yesterday will be reviewed next week.  Please check Illuminate to verify credit received for all work turned in.  If you think you have turned something in but have not received credit:

  1. Double-check your backpack, lab notebook, class folder, locker, and anywhere else you keep work.
  2. Check your returned work – it is possible I simply missed entering the grade into Illuminate.
  3. Ask to see the papers without names – I have several papers that were turned in without names.

Systems Biology – Lesson 12

In lesson 12, students learned about the systems of the human body.  After taking a quick pre-assessment, we watched a video explaining biological organization.  Organ systems were included in the hierarchy, and that led in to a second video about the human body.  Students were given a worksheet and each student was assigned one or two questions per video to answer.  At the end of the videos, everyone shared responses.  The final video focused on the respiratory system, and students followed along with the breathing exercises.  After the lesson, students received copies of two additional worksheets.  The first worksheet directed them to the website www.innerbody.com which they were instructed to use to learn about the various body systems.  The second worksheet guided students through the process of integrating their understanding of body systems relevant to the Heredity Project trait they completed as part of the Genetics Unit.  Students will have at least two additional class periods to complete the assignments from this lesson.

Systems Biology – Lesson 11

In this lesson, students were challenged to think outside the box.  With Odyssey sophomore and senior student defenses in full swing, students have been practicing the art of reflection.  As we transition from the study of ecosystems to the study of human body systems, we briefly returned to our study of financial ecosystems (lesson 3).  Students were introduced to the idea that our existing financial system is limited when it comes to integrating the value of natural resources.  We watched economist Pavan Sukhdev’s TED Talk “Putting a value on nature” where he explains the economic tools he uses to integrate natural resource valuations into his economic models.

We then transitioned to a discussion of cryptocurrencies as an alternative to traditional fiat currency.  I shared the final tally of the various eco-themed cryptocurrencies donated by generous members of the public in support of my biology students.  Students had previous elected to consolidate our crypto holdings into dogecoins, and I shared the news that each student could elect to receive either 5,650 dogecoins (currently valued at just under $3), $3 cash, or a free yearbook valued at $7.  About half of the students elected to receive their share of donated cryptocurrency, and I encouraged them to visit the Getting Started page.  Some students elected to set up accounts through Cryptsy, while others chose to receive their coins via the @tipdoge feature on Twitter.  Several students asked how they could spend their cryptocurrencies, so I explained that many retailers accept various currencies, including my good friend Bo Saxbe, operator of the Cheese Wizards sandwich truck.  A local news station recently profiled Cheese Wizards as part of a larger story about the first Bitcoin ATM to arrive in Seattle.  The cryptocurrency ecosystem is rapidly evolving, and it will be exciting to observe whether cryptocurrency will take hold and find a niche in the modern economy, or whether it will go extinct.

 

Systems Biology – Lesson 10

In lesson 10, we continued with our study of osmosis, focusing on the extreme environment of the Great Salt Lake.  Students learned that a railroad causeway was built across the lake more than 60 years ago, physically separating the lake into two sides.  Only the south side of the lake receives a continuous supply of freshwater, causing the salinity of the south side to be much lower than the north side.  As a result, the ecosystem of the south side of the lake is much more robust than the north side which is inhabited primarily be halobacteria.  Considered extremophiles because of their unique ability to live in extremely salty water, halobacteria are present in such abundance that they color the water in the north side of the lake purple (because of the rhodopsin protein they produce).  As evidence of their learning, students completed a case study worksheet and hypothesized what might happen to the existing Great Salt Lake ecosystem if the causeway were removed.

Systems Biology – Lesson 9

In lesson 9, our first lesson of the week, we circled back to osmosis, a concept students learned about early in the school year.  We connected the theme of “Water Follows Salt” with the reality that cell membranes contain pores and channels that regulate the flow of everything across the cell membrane.  We discussed the vocabulary of osmosis in the context of blood, recognizing that blood cells in plasma (isotonic) behave much differently than blood cells in water (hypotonic) or in saltwater (hypertonic).  We then thought about how salmon might be able to transition from freshwater to saltwater during their life cycle.  By connecting pore protein expression (via the Central Dogma) with evolution, students now have the foundation necessary to explain how salmon can hatch from an egg fertilized in a freshwater stream, migrate through the brackish waters of an estuary out into the Puget Sound, travel for years in the salty Pacific Ocean, and eventually find their way back to the steam from which they were born to complete their life cycle.   We wrapped up with a video about ice cave exploration, in which the concept of extremophiles was presented.  Students then transitioned to Work Time where they read an article and answered questions about extremophiles.

Systems Biology – Lesson 8

Our exploration of the Tyee Campus ecosystem concluded with a return to modeling energy flow using Microsoft Excel 2013.  Students worked individually to construct an energy flow model using a worksheet which provided the calorie requirements of a variety of organisms found on our campus.  The worksheet also included the Excel formulas to connect the various pieces of data into a model.  The lesson provided students with an opportunity to practice using the formula functions in Excel, taught them how to create a linked graph of the data, and asked them to derive explanations about why organisms are found in numbers approximating what might be anticipated by their understanding of the trophic pyramid.