KABT BioBlog

Looking for a new outdoor ecology investigation to conduct with your students?  … something that will require them to get their hands dirty?  … and aid in their learning and appreaciation for our native fauna? 

Then look no further than the new citizens science project, Earthworms Across Kansas organized by Dr. Bruce Snyder at Kansas State University.  As stated on their website and in an introductory letter I recieved a few weeks ago…

Earthworms Across Kansas is a free program that engages middle and high school students throughout the state in answering some basic, yet unanswered questions about Kansas earthworms, such as “Which species are here?” and “What are the ranges of these species?”

The project aims to educate Kansas’ middle and high school students about earthworm biology and invasive species issues by engaging them as citizen scientists.  One-third of the approximately 170 species of earthworms known to reside in the United States have arrived here from another continent.  We expect that most every earthworm your students collect will be an exotic species.

We are currently recruiting teachers to participate (online registration form), although only until we run out of kits.  Once registered, you can prepare for your participation by viewing curricula and lesson plans associated with earthworm biology that will be posted online through May.  In July or August your kit will be mailed, and your students can complete their collecting anytime during the 2010-2011 academic year.  The data from across the state will be uploaded on their interactive google map, and thus facilitate your students answering the basic questions posed by the project.

If you’d like more information about the program before registering certainly visit their website, and if you have further questions, please email the project at earthworm@k-state.edu.

I haven’t read through the protocols for this project yet but thought you may interested in learning from the active worm collectors and the research associated with their methods.  Check out Worm Grunting, Fiddling, and Charming—Humans Unknowingly Mimic a Predator to Harvest Bait published in PLOS.  Besides the article there are a number of interesting quicktime video links demonstrating the research.

At the NABT Conference in Atlanta in the fall of 2007, Brad Williamson talked me and a few others who were loitering around to come to a workshop presentation on Avida-Ed software as a means of fostering inquiry of evolutionary processes.  After the presentation, Brad suggested that I write a post about the experience.  At the time, I didn’t have much to say.

Having had time to play around with Avid-Ed and to make my way through most of the unedited model lessons downloadable from the Avida-Ed website, I have decided to make the post.  The best place to start is to download the software developed by Robert T. Pennock from the Avida-Ed website at Michigan State University, and to read the Discover magazine article written by Carl Zimmer highlighting Robert Pennock’s development and use of the research version of the software to study the process of evolution (The first activity below has pre-activity questions that require students to read this article).  The links below will get you that far.

1. Avida-Ed Website
2. Testing Darwin by Carl Zimmer in February 2005 edition of Discover magazine.

If you are a self learner, after downloading the Avida-Ed, open it, drag the @ancestor into the black area of the Petri Dish window to the right, select the play button, and have fun.  Otherwise, keep reading…

Well, as I said, I have had the time to make my way through the unedited model lessons posted on the Avida-Ed website.  In effort to prepare to introduce my freshman honors biology and AP Biology student for the software, I have cut and pasted, edited, and created (in some cases) more detailed step-by-step instructions for the activities presented in their models lesson.  In a few cases, I have even collected and attached data in a teachers section at the end of the student friendly documents that help you understand what the students will be doing prior to your own exploration of the software.

Explorations in Evolution Series

1. I – Introduction to Avida-Ed
2. II – Observing an Instance of Evolution in Avida-Ed
3. III – How do Resource Availability & Mutation Rate influence Avidian Fitness?
4. IV – Observing Mutations in the Genomes of Evolving Avidians
5. V – Common Misconceptions of Evolution

I look forward to your comments and criticism of the activities but realize that I am just beginning to use these activities in my class for a second time.

As a justification for activities such as these, if you take the time to read the Bio2010 published by the National Academies as well as the most recent bulletin from HHMI (read Thinking like an Engineer and Add 56), you will quickly learn that we should be doing more to motivate our keen biology students to appreciate the importance of other scientific perspectives (mathematics, computer science, physic and engineering).  Similarly, we should be reaching out equally to those that are already bent toward study in these other fields and show them that they can fulfill there interests while helping to make new discoveries in the biological sciences.

Download the non-education version of Avida.

Enjoy!

Before the weekend, I received an e-mail from a colleague asking “Do you know of a good place I can go gather termites… anywhere woody?”

I responded with my suggestions, and because I was intrigued, I replied with a question of my own, “What do you plan to do with them?”

Well, after a making my own way through portions of two decaying logs, and acquiring some special and not-s0-special writing utensils, see what we ended up witnessing by watching the following videos… 

1. Termite and paper (30 sec.)
2. Termite, paper, and pencil drawn Infinity (30 sec.)
3. Termite, paper, and Sanford Uniball Black drawn Infinity (30 sec.)
4. Termite, paper, and Papermate Red drawn Infinity (30 sec.)
5. Termite, paper, and Papermate Red drawn Spiral (30 sec.)

Sorry for the out-of-focus imagery but I hope these 2.5 minutes of observation motivate you as much as they did us before we introduced these creature to our classes today!  Experiment with other colors, other writing utensils, and have fun googling to see what is already known about the behavior you witnessed.

Happy Inquiry!

While learning about those involved in developing the Synthetic Biology survey that some of you may have taken (June 8th post), I serendipitously navigated to a page at Davidson College that made me aware of the Microarrays MediaBook educational website.  Here is what I read, including the link that I chose to follow…

Another of Malcolm Campbell’s efforts, a multimedia presentation entitled “MicroArrays MediaBook,” has received the international Pirelli Award as the “Best Work for Educational Institutions.” Created with collaborators at UNC Chapel Hill, the MicroArrays MediaBook shows students how microarrays are created and analyzed, and applications of the technology. Its graphic sophistication commands attention, and students can test their understanding of the material with questions for each section.

Here is a shot of the homepage with their extensive internal links.  I agree that the “graphic sophistication commands attention”.  I’m still checking it all out and already know that if you touch upon Microarrays in your classroom you should spend sometime this summer checking it out as well…

http://gcat.davidson.edu/Pirelli/index.htm

Here is an paper activity that I have used to teach about Microarrays, a link to the article that I use with the activity, although I think I will be modifying things so that students can use the MediaBook resources instead.  For those beyond a paper activity, Fotodyne has microarray kits for exploring smoking and plant photobiology, and the Genome Consortium for Active Teaching (GCAT) has a wealth of information and resources for developing authentic microarrays (also developed by Malcolm Campbell).

As my father always says, enjoy!

 Cellular Respiration Lab with Grass Seed

This is a version of the AP Biology respiration lab that I’ve modified to be quicker and easier to accomplish in limited class time.  It also is teachers like me who realize at the last minute that they’re planning to do a lab for which a key supply is difficult to come by in a rush.  I’ve had problems a couple of times finding good seeds to use in the fall – grocery store beans have at times done a better job of growing fungus for me than of germinating.  In the fall in the midwest, the easiest and cheapest seeds to find that are guaranteed to germinate are grass seeds so that’s what I used for this lab. 

I had student aides mass out the seeds for me (into plastic petri dishes with dry paper towels cut to fit into the bottom of the petri dishes).  Then all I had to do was add enough water to thoroughly moisten the seeds (and towels) in half the petri dishes that evening before leaving school.  (Don’t forget to leave half of them dry – these are your dormant/non-germinating seeds.)  In the morning I checked the seeds again to make sure they were thoroughly moist but not too wet and continued to periodically check them until we used them in the lab. 

With this modification the lab went very smoothly and seeds begun on Monday after school were adequately germinated by mid-morning that Thursday (and perfect for the Friday classes).  I realize it’s better to keep the volume of seeds (and beads) constant in all the respirometers but most of my students fail to appreciate that subtlety and often get so wrapped up in technique that they miss the key concept – the changing oxygen volumes.  This version seemed to work well with those students.

 Cellular Respiration Lab with Grass Seed

Catalase Enzyme Activity Lab

This Catalase Enzyme Activity Lab has a technique which is easy for students (after the initial practice phase) and lets them gather multiple trials quickly and easily.  It’s powerful because it allows exploration of important biochemistry concepts while reinforcing data analysis and utilizing graphing techniques tested on state math assessments.

Each group explores one set of conditions in detail then uses the data of other groups to graph and analyze several other conditions.  I use this lab early in the year when I’m working on protein structure, enzymes, and how free energy relates to enzyme activity.  The lab utilizes filter paper disks (cut out with a hole punch to keep them uniform sizes) dipped in catalase solutions which are then dropped into hydrogen peroxide.  Students time how long it takes for the disks to rise (they rise when enough oxygen bubbles accumulate on the filter disks to make them buoyant in the hydrogen peroxide solution).  The data produced is easily graphed and analyzed using box and whiskers graphs (aka box plots).   Students are taught this graphing technique in math classes (and are tested on it on state assessments) but don’t often have the opportunity to apply them and therefore don’t appreciate their ease, elegance, and power.

Catalase Enzyme Activity Lab

I’ve been cleaning up one of my old web pages and I ran across this instructional page my students constructed several years ago after completing a lab on onion root tip mitosis. Thought it might be of use since I’ll be closing out the old web page, soon. I’ll be updating this lab with new and improved images later but for now here’s the original document with its ancient digital images…

Onion Root Tip Mitosis

Adapted from:

Babich, H., Segall, M.A. and Fox, K.D. (1997). The Allium Test–A Simple, Eukaryote Geneotoxicity Assay. The American Biology Teacher. 59, 580-583.

Materials:

• Test tube (13x100mm)
• fixative (9 part 45% acetic acid and 1part 1N HCL)
• watch glass
• onion
• beaker or small cup (150mL, approximately)
• scissors
• razor blade
• metal spatula
• aceto-orcein stain
• microscope slides
• cover slips.

Stain preparation: 5 g of orcein is added 150 ml of hot acetic acid. Keep the stain solution in a dark bottle for 2-3 days , shaking several times to saturate the solution. After that treatment, add 150 ml of distilled water, filter and store in a dark bottle. (Babich, Segall and Fox, 1997)

Procedure:

Growing Onion Root Tips

Obtain onion bulb, four toothpicks, small beaker (150mL), and enough water to fill the beaker to top. Hold the onion by the top, insert four toothpicks at perpendicular angles to suspend onion into the water. Wait two or three days for root tips to grow.

Harvesting and Fixing the Root Tips:

Obtain test tube, pair of scissors, watch glass, and fixative (9 parts 45% acetic acid and 1 part HCL).

Cut off four root tips, each approximately 1 cm long; Fill test tube 3cm full of fixative.

Place four root tips into the test tube of fixative and incubate at 50 degrees Celsius for six minutes. Then dump heated fixative and tips into watch glass.

Staining the Cells:

Take root tips, one at a time, out of watch glass and place each on in the middle of a microscope slide.

Cut all excess from the root tips except for 2mm at the very tip of the root (end that was not cut from the plant).

Place two drops of aceto-orcein stain on top of the 2mm root tip.

Let stain soak into root tip for two minutes.

Squash the root tip, on each slide, pressing straight down so as not to overlap the cells.

Place two more drops of stain upon the root tip and wait for another two minutes.

Then place cover slip flat upon the root tip, making certain not to move the cover slip horizontally.

Press the cover slip gently with a pencil eraser, again only straight down without moving the cover slip.

Soak up extra stain from slide around cover slip with a paper towel without moving cover slip.

Observe and record steps of cell division under microscope (at 400x)

Sample views at 400x:

A request on the AP Biology list for a lab write-up for the floating disk assay prompted me to make an old lab performance assessment (exploring-photosynthesis-lab-test) that I wrote several years ago available for download. It’s not a lab procedure per se but it can serve as one. It is certainly not written as an AP Lab substitute but should get someone started if they need some extra prompting.

BTW, I have to admit I just uploaded this and did not check it out for rewrites or edits. If you find egregious errors or even a bit of misguiding–let me know and I’ll see what I can do.

BW

Last night, on the AP-Bio listserv a teacher asked about trouble with sinking leaf disks for the Floating Leaf Disk lab. Her class had difficulty getting the spinach leaf disks to sink. I offered some possible solutions and I also promised to post a video of the procedure in case the students were missing something in the written protocol. Here’s the quick video that I made this morning.

Google video seems to be down this morning (Sept. 30). If this continues I’ll upload the video to a different service–stay tuned.

BW

This post is meant to inform those unable to attend the Dolan DNA Learning Center workshop at the Stowers Institute on Genes to Cognition.  This is a site that you will want to delve into when you have a bit of time on your hands.  Well, that is if you are interested in learning and teaching about the connect between genes, cognitive behaviors, and their related brain disorders. 

The student-friendly essential question that this site helps students and teachers to explore is, “What good is a brain?” 

In all honesty, the site reminds me of Thomas Huxley’s book The Crayfish through which he demonstrates that the subject of zoology could be taught via a single model organism. 

In a similar manner, Genes to Cognition facilitates the teaching of biology at all levels of complexity, from the molecular communication networks of our cells to the behaviors that emerge from their collective actions.  At the same time, students will realize that there are numerous unanswered scientific questions awaiting research.

Having had little time to digest the material presented, I currently don’t know where I will integrate Genes to Cognition into my courses but “What good is a brain?” it is quite an appropriate question for students to ask and begin to explore.  The site is presented from a perspective that, on one hand acknowledges the importance of the reductionist approach, while fostering the burgeoning systems based perspective.

Genes to Cognition Website

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