TBT: Protein Synthesis Models (In My Classroom)


Thanks to a little idea from Brad I thought I would try something with my AP Biology students this week that I saw him try with his BIO 100 students at KU earlier.

We’re currently marching our way through the mind-bending terror that is protein synthesis. So we’ve gone over the whole process a bit but to make sure we were not getting lost in the details I gave them this:

Blank central dogma 1Blank central dogma 2

Two different models of the same process. Nothing earth-shatteringly innovative but how I framed it and worked with it was unique to me. I didn’t just say it was a worksheet to complete. I framed it as 2 different models of the same process. If they wanted to use the picture in their book that was ok because the diagram in their Campbell book also looked different. What I was surprised with was how much students struggle translating [pun] knowledge across models. Students struggled with labeling processes versus structures, labeling the same structure that was differently drawn in two models, and especially when one model added or removed details (like introns and exons).

The other cool part was that afterwards when students shared their answers on the board, they had lengthy discussion about what was “right”. For example, two students argued whether the 4th answer from the top was “pre-mRNA” or “mRNA” and explained why they thought that. After looking to me I shared that by their explanations both could be right. That’s what I think was cool, students argued different answers where with the proper explanations, either could be right. So because of that, I would avoid giving an “word bank”.

Also, at the very end I created a list on the board titled “limitations” and I had them share what was limiting about these diagrams. Some thoughts were “no nucleotides were shown entering RNA polymerase”, “no other cell components were shown”, “the ribosome on top only had room for one tRNA”, “no mRNA cap or tail were shown”, and many more.

I found this exercise useful because I struggle giving students modeling opportunities (especially non-physical ones) and this was a simple way for students to get practice comparing/contrasting models while also discussing the usefulness and limitations of them.

Alright, for the 4th installment I nominate el presidente himself, Noah Busch.

A 3D Gene Expression Lesson on Epigenetics

Disclaimer: As far as standards go, I really like the Next Generation Science Standards. Particularly important to me is the emphasis it places on learning not just the content (disciplinary core ideas), but how scientists work/think (science practices) and connections between ideas (cross-cutting concepts). Over the last 3-4 years, I have been giving my favorite activities and labs an NGSS facelift to modify them to better fit this framework. I am going to share with you a lesson that I feel address all 3 dimensions of the NGSS.


Is your lesson “3D”? Use the NGSS Lesson Screener tool to find out.  LINK

Many students really enjoy their genetics units, but one of the more difficult things to understand is gene expression. Several years ago, I would have presented my students with the “central dogma”, given some notes over transcription and translation, then worked through a few scaffolds to get them to understand how amino acid chains are produced. After reading Survival of the Sickest in 2008, I started to mention that epigenetics was a thing, though I didn’t have my students investigate it with any depth.

With the introduction of the Next Generation Science Standards, an emphasis has been placed on understanding the implications of the processes in the classic dogma without getting overly concerned about what specific enzymes might be doing at a given time. This has freed up more time to explore the regulation of gene expression, including epigenetics. There are a number of amazing resources out there (like this… and this… and this…), but here is how I cover gene regulation with my 9th grade biology students:

This format is something I have adapted (with few changes) from an NGSS training put on by Matt Krehbiel and Stephen Moulding, which I attended thanks to KSDE. I like this because it is flexible, provides students with the entire trajectory of the lesson from the beginning, and can double as a lesson plan. Can you guess the reasoning behind the color-coded words? That, too, is explicit, though it is in most cases more for my own benefit. RED words are commands for the students. It tells them how they should address the problem and how I will assess their work. The GREEN words relate to cross-cutting concepts (in this case, systems/system models and patterns), while the BLUE(ish) words are science practices.

Depending on how much time you have available, this could take 2 to 4 50-minute class periods (or 1-2 block periods if you’re lucky enough to roll with that schedule).  I like to use more time for this because I have designed discussion and collaboration into the process, but the “Gather Information” and (obviously) “Individual Performance” sections could be done by students on their own and wouldn’t require a classroom. Devoting a little extra class time will also allow for you to conduct ad hoc informal formative assessments (read over a kid’s shoulder and ask them questions) as you move around your room.

Part 1: Gathering Information

Have you listened to the RadioLab episode, “Inheritance”? If not, you should do that. I find that RL is a good way to indoctrinate your students into the world of science podcasts. And this episode is one of my favorites. 

I really like reading with my students, asking them questions that get them thinking deeper as they go, so I usually devote an entire class period to reading an article on epigenetics. I break my class into three groups with each group reading a different article, and students will (for the most part) self-select based on the length or difficulty of the reading.  I use readings pulled from Discover Magazine, Nature Education, Nat Geo’s Phenomena blogs. Students sit around large tables and talk and write and sketch as they read. There is structure and agency, direction and freedom, and I love those days. But if you’re in a hurry (in my opinion, one of the worst reasons to do something), I guess you could assign the reading as homework.


Part 2: Thinking Deeper

To really understand something, you need to really dig into it. This section is meant to be collaborative. If I have some really outstanding students grouped together, I will encourage them to divide the work in this section between them, then teach their group members in a scaffold.  I wouldn’t normally do this with an extension/research-based activity because I want to make sure each student has a chance to interact with each aspect of the activity. If I can’t trust all the group members to produce the same quality of work, I won’t recommend the divide-and-conquer approach.

When dealing with my AP/College Biology students, I would word a question like #5 differently. With the general biology kids, I recognize most of them will not end up in a biology-centric career. They will, however, be citizens of the world, and voters. So I try to incorporate questions where they reflect on their emotional response to the content. I know it is popular to think of scientists as unfeeling, opinion-less automatons, but that is disingenuous. I live with a scientist, trust me. I use experiences like this to really emphasize the importance of evidence-based, empirical thinking and using data to drive decision-making.

Part 3: Individual Performance

How do you know if your students “get it”?  A lot of the time, when using a science notebook or interactive journal, it might be several days before you go back and read everything your students wrote (and maybe, sometimes, you still don’t read everything). What I like to do is tell students they will have 15 minutes to produce the best possible answer after I give them 5 minutes to discuss with their classmates how they will address the last couple of items for this assignment. Once the writing starts, I am walking the room, reading over shoulders, and looking for patterns. Are there any things that I think they should have gotten, but most people are missing? Are we particularly strong in certain areas? Are students adding models to their answers in support? This lets me know if I need to reteach something or if we can move on.

I also look for answers that are good, but might be missing one bit of information to take it over-the-top. It is a good rule of thumb to think that, if one student is making a mistake, there are other students making the same error. I will then (not so) randomly ask students to read exactly what they have written down. By using an answer that is mostly correct, it takes some of the stigma away from making a mistake. We can then have a discussion with the class to see if we can identify where the answer can be changed or added to, and praise the parts of the answer that were done well. Students with sub-par responses are encouraged to add to their answers, and we learn more together.


If you are still with me, what do you think? What does this activity do well? Where can I get better? What are my students missing? If you would like to modify/use this activity, you can find a GoogleSlides version here. Send me an email (andrewising[at]gmail) or tweet (@ItsIsing) and let me know how it went!

Summary Post for Teaching Quantitative Skills

Part 1: Teaching Quantitative Skills using the Floating Disk Catalase Lab: Intro
Part 2- Teaching Quantitative Skills in a Lab Context: Getting Started in the Classroom
Part 3- Establishing an Experimental Procedure to Guide the Home Investigation
Part 4- Teaching Quantitative Skills: Data Analysis
Part 5- Curve Fitting AKA Model Fitting–the End Goal
Part 6- The Final Installment: Extending and Evaluating Quantitative Skills.

These are links to the posts on Teaching Quantitative Skills with the Floating Disk Enzyme Lab

  1. http://www.kabt.org/2016/11/29/teaching-quantitative-skills-using-the-floating-disk-catalase-lab-intro/
  2. http://www.kabt.org/2016/12/01/teaching-quantitative-skills-in-a-lab-context-getting-started-in-the-classroom/
  3. http://www.kabt.org/2016/12/04/establishing-an-experimental-procedure-to-guide-the-home-investigation/
  4. http://www.kabt.org/2016/12/09/data-analysis/
  5. http://www.kabt.org/2016/12/18/curve-fitting-aka-model-fitting-the-end-goal/
  6. http://www.kabt.org/2017/01/06/the-final-installment-extending-and-evaluating-quantitative-skills/

Curve Fitting AKA Model Fitting–the End Goal

Curve Fitting AKA Model Fitting:
When I started this series of posts my goal was to see if I could generate precise data with a proven classroom lab.  The data precision that is possible with the yeast catalase lab provides a unique opportunity where data analysis skills can be productively explored, practiced and understood.  My contention was that this is the ideal lab to focus not just on content, not just on experimental design, but also to introduce relatively sophisticated data analysis.  To be up front about it, I had only a hint of how rich this lab is for doing just that.  Partly , this is because in my years of teaching high school biology I covered most of the enzyme content in class activities and with 3D visualizations, focusing on the shape of enzymes but neglecting enzyme kinetics.  That would be different if I were teaching today—I’d focus more on the quantitative aspects.  Why?  Well, it isn’t just to introduce the skills but it has more to do with how quantitative methods help to build a deeper understanding of the phenomena you are trying to study.  My claim is that your students will develop a deeper understanding of enzymes and how enzymes work in the grand scheme of things if they follow learning paths that are guided and supported by quantitative data.  This post is an example.
The last post focused on plotting the data points as rates, along with some indication of the variability in each measurement in a plot like this.
As I said before, I would certainly be happy if most of my students got to this point as long as they understood how this graph helps them to describe enzyme reactions and interpret others work.
But a graph like this begs to have a line of best fit–a curve that perhaps plots the relationship implied by our data points.
Something like this.

One of the early lessons on model building in my current Research Methods course involves taking data we have generated with a manipulative model (radioactive decay) to generate a predictive model.  The students plot their data points and then try to find the mathematical expression that will describe the process best.  Almost always, my students ask EXCEL to generate a line of best fit based on the data.  Sometimes they pick linear plots, sometimes exponential, sometimes log plots and sometime power plots.  These are all options in EXCEL to try and fit the data to some mathematical expression.  It should be obvious that the process of exponential decay is not best predicted with multiple types of expressions.  There should be one type of expression that most closely fits the actual physical phenomenon–a way of capturing what is actually going on.  Just picking a “treandline” based on how well it visually fits the current data without considering the actual phenomenon is a very common error or misconception.  You see, to pick or develop the best expression requires a deep understanding of the process being described.  In my half-life exercise, I have the students go back and consider the fundamental things or core principles that are going on.  Much like the process described by Jungck, Gaff and Weisstein:

“By linking mathematical manipulative models in a four-step process—1) use of physical manipulatives, 2) interactive exploration of computer simulations, 3) derivation of mathematical relationships from core principles, and 4) analysis of real data sets…”
Jungck, John R., Holly Gaff, and Anton E. Weisstein. “Mathematical manipulative models: In defense of “Beanbag Biology”.” CBE-Life Sciences Education 9.3 (2010): 201-211.
The point is that we are really fitting curves or finding a curve of best fit–we are really trying to see how well our model will fit the real data.  And that is why fitting this model takes this lab to an entirely new level.   But how are you going to build this mathematical model?
Remember that we started with models that were more conceptual or manipulative.  And we introduced a symbolic model as well that captured the core principles of enzyme action:

By Thomas Shafee (Own work) [CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons
Now how do we derive a mathematical expression from this?  I’m not suggesting that you should necessarily unless you feel comfortable doing so but I’ll bet there are kids in your class that can given a bit of guidance.  You may not feel comfortable providing the guidance.  But in this day of “just ask Google” you can provide that guidance in the form of a video discussion from the Khan Academy designed to help students prepare for the MCAT.  Don’t let that scare you off.  Here are two links that take the symbolic model and derive a mathematical expression–not just any expression—the Michaelis-Menten equation for enzyme kinetics. You or your students will no doubt need to view these more than once but the math is not that deep—not if your students are exploring calculus or advanced algebra.  It is really more about making assumptions and how those assumptions simplify things so that with regular algebra you can generate the Michaelis-Menten equation.
You can also find a worked out derivation here:  https://www.ncbi.nlm.nih.gov/books/NBK22430/  in this text excerpt from Biochemistry, 5th ed. Berg JM, Tymoczko JL, Stryer L.
New York: W H Freeman; 2002.
Of course, you don’t even have to go through the derivation you could just provide the equation.

The important thing is that students understand where this equation comes from—it doesn’t come out of thin air and it is based on the same core principles they uncovered or experienced if they did the toothpickase manipulation–it is just quantified now.  So how do I use this equation to actually see how well my data “fits”?  If it were a linear expression that would be easy in Excel or any spreadsheet package but what about non-linear trend lines?  I can tell you that this expression is not part of the trend line package you’ll find in spreadsheets.
I’ve got to admit, I spent too many years thinking that generating best-fit curves from non-linear expressions like the M-M equation was beyond the abilities of me or my students.  But again “Ask Google” comes to the rescue.  If you google “using solver for non-linear curve fitting regression” you’ll end up with lots of videos and even some specific to the Michaelis-Menten equation.  It turns out EXCEL (and I understand Google Sheets) has an add-on called Solver that helps you find the best fit line.  But what does that mean?  Well it means that you need to manipulate the parameters in the M-M equation to generate a line until it mostly fits your data–to see if the model is an accurate description of what you measured.  What parameters are these?
Look at the equation:
V0 equals the rate of the reaction at differing substrate concentrations–the vertical axis in the plots above.
Vmax equals the point at which all of the enzyme is complexed with the substrate–the maximum rate of the reaction with this particular enzyme at this particular enzyme concentration (that is enzyme concentration not substrate)

Km equals the concentration of the substrate where the rate of reaction is 1/2 of Vmax

[S]  equals the substrate concentration, in this case the H2O2
Two of these parameters are variables—one is our experimental or explanatory variable, the concentration of H2O2 and the other is our response variable, the rate of the reaction. Some folks prefer independent and dependent variable. This is what we graph on our axis.
The other two parameters are constants and the help to define the curve. More importantly, these are constants for this particular enzyme at this particular enzyme concentration for this particular reaction. These constants will be for different enzymes, different concentrations or reactions with inhibitors, competitors, etc. In other words it is these constants that help us to define our enzyme properties and provide a quantitative way to compare enzymes and enzyme reactions. You can google up tables of these values on the web. from: Biochemistry, 5th ed. Berg JM, Tymoczko JL, Stryer L.
So calculating these constants is a big deal and one that is not typically a goal in introductory biology but if you’ve come this far then why not?
This is where generating that line that best-fits the data based on the Michaelis-Menten equation comes in.
You can do this manually with some help from Solver in Excel.  (Google Sheets also is supposed to have a solver available but I haven’t tried it.
I have put together a short video on how to do this in Excel based on the data I generated for this lab.

I’ve also taken advantage of a web based math application DESMOS which is kind of a graphing calculator on the web.  While I can create sliders to manipulate the constants in the equation, Km and Vmax  to make a dynamic spreadsheet model it is a lot easier in DESMOS and DESMOS lets me share or embed the interactive equation. Scroll down in the left hand column to get to the sliders that change the constants.

You can also just go to Desmos and play with it there

I had to use A and B and x1 in my equation as symbols.

It is not that difficult to use DESMOS and with my example your students who are familiar with it will be able to make their own model with their own data within DESMOS.  Move the sliders around—they represent the values for   Km and Vmax  in the equation.  Notice how they change the shape of the graph.  This really brings home the point of how these constants can be used to quantitatively describe the properties of an enzyme and helps to make sense of the tables one finds about enzyme activity.  Also, notice the residuals that are plotted in green along the “x-axis”.  These residuals are how we fit the curve.  Each green dot is the result of taking the difference between the a point on theoretical line with particular constants and variable values and the actual data point.  That difference is squared.  A fit that puts the green dots close to zero is a very good fit.  (BTW, this is the same thing we do in EXCEL with the Solver tool.)  Watch as you try to minimize the total residuals as you move the sliders.  The other thing that you get with DESMOS is that if you zoom out you’ll find that this expression is actually a hyperbolic tangent…and not an exponential.  How is that important?

Well, think back to the beginning of this post when I talked about how my students often just choose their mathematical model on what line seems to fit the data the best–not on an equation developed from first principles like the Michaelis-Menten.

Looking at a plot of the data in this experiment before the curve fitting one might have proposed that an exponential equation might have produced the best fit.  In fact, I tried that out just for kicks.
This is what I got.

Here’s a close-up:

Thinking about the actual experiment and the properties of enzymes there are two things really wrong with this fit although you’ll notice that the “line” seems to go through the data points better than the fit to the Michaelis-Menten equation.  1.  Notice that the model line doesn’t go through zero.   Hmmmm.  Wouldn’t a solution with no Hydrogen peroxide not react with the yeast?  That should be tested by the students as a control as part of the experimental design but I can tell you that the disk will not rise in plain water so the plot line needs to go through the origin.  I can force that which I have in this fit:

But the second issue with this fit is still there.  That is the point where the plot has reached it’s maximum rate.  If I had generated data at a 3% substrate concentration I can promise you the rate would have been higher than 0.21 where this plot levels off.  While the exponential model looks like a good fit on first inspection it doesn’t hold up to closer inspection.  Most importantly the fit is mostly coincidental and not base on an equation developed from first principles.  By fitting the data to the mathematical model your students complete the modeling cycle described on page T34 in the AP Biology Investigative Labs Manual, in the Bean Biology paper cited above, and on page 85 in the AP Biology Quantitative Skills Guide.
Give model fitting a try—perhaps a little bit a time and not all at once.  Consider trying it out for yourself with data your students have generated or consider it as a way of differentiating you instruction.  I’ll wrap this up with a model fitted with data from Bob Kuhn’s class that they generated just this month.  He posted the data on the AP Biology forum and I created the fit.

The key thing here is that his enzyme concentration (yeast concentration) was quite a bit diluted compared to the data that I’ve been sharing.  Note how that has changed the Michaelis-Menten curve and note how knowing the Km and Vmax provides a quantitative way to actually compare these results.   (Both constants for this graph are different than for mine)
Hopefully, this sparks some questions for you and your students and opens up new paths for exploring enzymes in the classroom.  I’ll wrap this up next week with how one might assess student learning with one more modeling example.

Model Building and Building on Models

I make my students build and use models on a daily basis in my classrooms. I think that I have a better than average grasp on the Next Generation Science Standards, their practice and three-dimensional lesson planning. But I have apparently never thought to throw a bunch of vocabulary words at my students and give them the time to really struggle to connect them into a cohesive model with their groups.  And at the end of a session on Cognitive Models, presented by AP/IB Biology teachers Lee Ferguson and Ryan Reardon, that is exactly what we did.


To start, the instructions were sparse: Create connections and uncover relationships between pancreatic β-cells and photosynthesis. My group was made up of six other AP Biology teachers from 4 states, none of us with any idea where to start. There was some discussion about the significance of the color of each card, which it ends up wasn’t important… there just wasn’t time to sort them before the session.  We eventually found the word “Metabolism”, which we all agreed was the one thing that all the cards shared. From there, we tried to make shorter stacks of cards that were related. For example, “Hyperglycemia”, “Blood sugar rises”, and “insulin”.

Once we had all the cards grouped, we tried to place them into a pseudo-concept map. In our classrooms, I would have probably done this on a big whiteboard so we could draw arrows and write connecting terms, but my group guess that the Sheridan didn’t want us writing on their table cloths. 🙂  As we went, we had to stop and rearrange our map several times and each time we edited the map, members of the group were justifying why some cards had to stay or move.  It was a really great conversation and I learned some things about feedback loops that I don’t think I had ever known.

At the end of the process, we were encouraged to go look at what the other tables had put together and reflect on our map. To my surprise, none of the other groups had anything resembling our model. Talking to some of the other groups, I don’t think that anyone had a model that I think failed to achieve the original objective. It was really a powerful reminder that students, no matter the amount of information they may possess, each approach a problem from a unique viewpoint. And when you have people put together information, even people that all know “the right answer”, there are many ways to arrive at that conclusion.

Needless to say, next week when we start preparing for our next test in my 9th grade Biology class, my students are getting a stack of 3×5 cards tossed on to their tables. I can’t wait to hear their conversations and see what they create!

This post is part of a series of posts from KABT members reflecting on some of the most important things they’ll bring back into their classrooms from the NABT 2016 Professional Development Conference.

TBT: Miniposters

Editor’s Note: So far this semester, the most popular single post on the BioBlog is this September 2013 peer-review piece from our blogfather, Brad Williamson. Also this is a reposting of a reposting. Blogception!  Enjoy this, and if you use mini-posters in your classes, share your experience with us in the comments!

This is a reposting of a post that first appeared on the NABT BioBlog:

Miniposter, Jai Hoyer

Background and Rationale:

Almost 20 years ago, I was fortunate to be invited to my first Bioquest Workshop at Beloit College. Maura Flannery covered the Bioquest experience in several her columns in the American Biology Teacher. These workshops challenge and inspire you as you work with a number of like-minded biology educators working on the edge of new developments. What really caught me off guard was the intensity of the learning experience. Before the end of the first full day, each working group had to produce a scientific poster presentation. This was my first, personal experience with building a poster so I’m glad that I don’t really have a record of it. I talked to John Jungck about the poster requirements—he told me that the students in his labs prepare a poster for each laboratory–rather than a lab-write up and they have to defend/present them in poster sessions. I immediately saw that a poster would help me evaluate my student’s lab experience while provide a bit of authenticity to my students doing science. That fall I had my students do a poster session that was displayed in the science hall. It was a big success with one exception. For my high school class, the experience was a bit too intense and too time consuming. It turned out that we could only work in one big poster session that year. One of the little bits of clarity of thought that comes from teaching for decades instead of years is the realization that students need to practice, practice, practice—doing anything just once is not enough. I thought about abandoning the poster session since it was too time consuming. However, I witness great learning by all levels of students with this tool. I didn’t want to abandon it. With this thought rolling around in my mind, I was primed as I visited one of my wife, Carol’s, teacher workshops. She’s a science teacher, too. In this workshop she was presenting an idea to help elementary teachers develop science fair project—a mini-science fair poster. This idea involved the used of a trifolded piece of 11″ x 17″ paper. The teachers were inputting their “required” science fair heading with post-it notes. Revision was a breeze. The teachers learned the importance of brevity with completion. They added graphs and images by gluing their graph to a small post-it. It was all so tidy, so elegant, so inviting, I probably stared a little long, struck dumb by the simplicity of the mini-poster. Once I came to my senses I realized that the mini-poster was my answer–a way to incorporate authentic peer review, formative assessment in my science classes. My high school classes could be like John’s college classes.

Making Miniposters

Over the years, mini-posters have evolved into the following. We take two, colored (for aesthetics file folders, trim off the tabs and glue them so that one panel from each overlap—leaving a trifold, mini-poster framework. Each student gets one of these. For these posters we go ahead and permanently glue on miniposter-headers that include prompts to remind the students what should be included in each section. Later, they can design their own posters from scratch. The image at the top of the page and the ones following will give you an idea. By using post-it notes the posters can easily be revised and we also reuse the poster template several times over the year. Don’t feel that you have to follow this design–feel free to innovate.

Implementing Mini-posters:

Defending the Miniposter–Presentation

Defending the miniposter:
For the first mini-poster experience, I give my students as much as a class period to work up a poster after completing an original research investigation. (We do quite a few of these early in the school year with others periodically throughout the rest of the year). Sometimes poster work is by groups and sometimes by individuals. Once the posters are ready, the class has a mini-poster session. The class is divided up in half or in groups. Half the class (or a fraction) then stays with their posters to defend and explain them while the other half play the part of the critical audience. To guide the critic, I provide each “evaluator” with a one page RUBRIC and require them to score the poster after a short presentation. I restrict the “presentation” to about 5 minutes and make sure that there is an audience for every poster. We then rotate around the room through a couple of rounds before switching places. The poster presenters become the critical audience and the evaluators become presenters. We then repeat the process. By the end of the hour every poster has been peer-reviewed and scored with a rubric–formative assessment at its best. The atmosphere is really jumping with the students generally enjoying presenting their original work to their peers. The feedback is impressive. At this point I step in and point out that I will be evaluating their posters for a grade (summative assessment) but they have until tomorrow (or next week) to revise their posters based on peer review—oh, and I’ll use the same rubric. The process works very well for me and my students and my guess is that it will for yours as well. You’ll naturally have to tweak it a bit—please do. If you find mini-posters work for you, come back here and leave a comment.

The images are from our UKanTeach Research Methods course first assignment—a weekend research investigation. Thanks to the Research Methods course for the images.

Another Sample Miniposter: Artificial Selction of Trichomes in Fastplants

Here’s a file that illustrates what a Sample-miniposter might look like constructed in MS Word.

Links to websites for advice on making scientific posters:





In My Classroom: Investigating Energy Flow with ZOMBIES!

Welcome to the KABT blog segment, “In My Classroom”. This is a segment that will post about every two weeks from a different member. In 250 words or less, share one thing that you are currently doing in your classroom. That’s it.

The idea is that we all do cool stuff in our rooms and to some people there have been cool things so long that it feels like they are old news. However, there are new teachers that may be hearing things for the first time and veterans that benefit from reminders. So let’s share things, new and old alike. When you’re tagged you have two weeks to post the next entry. Your established staple of a lab or idea might be just what someone needs. So be brief, be timely and share it out! Here we go:

Investigating Energy Flow with ZOMBIES!


The Set-Up

It’s the zombie apocalypse! You have a safe fenced-in area that is impenetrable to the zombies.  But, you also cannot leave the fenced in area. If you had time to prepare this land, what would you plant? What livestock would you have? (Note: Students have the option of doing a Mars Biodome if they do not want to do the zombie apocalypse.)

Student groups are all given the same 11 x 17 inch grid paper. Each square equals 100 square feet. Each student needs a housing structure(s) that equal 20×25 squares.


The Goal

Sustain as many humans as possible using the land space given. The group who can sustain the highest number of people wins. The criteria for sustainability is 2,000 calories per day, per adult (730,000 calories per year). (Note: No stockpiling allowed).

The Work

Students need to find the total number of producer calories from all their crops. (Find the calories / square foot for each food, and then multiple by the number of total square feet.)


Then, students need to calculate how many of those producer calories are actually available for human consumption. To do so, students must figuring out how many of those producer calories their livestock will consume per year.


The only livestock here was goats, if you have different species of livestock you’ll want to add those together to do this calculation.

Next, students need to find the total number of anaimal calories produced. They calculate how many calories of meat (or eggs/dairy) each animal produces. (To simplify, one could assume the entire weight of the animal is meat.) Students do this for each type of livestock and add it together to find the total number of livestock calories produced. (If you have any secondary consumers, they will take a whole other set of calculations!)

Next, students find out how many calories their land produced for human consumption. They take the number of plant calories available for humans and add it to the total number of animal calories produced. Then, they divide that by 730,000 (the total number of calories needed per human per year) to see how many humans they can support.


Getting the Numbers

To make it easier, you could provide a list of several crop and livestock options with their calorie information. But, for me, one of the best parts of this project was having it open ended for the students. I have my students find the information on their own, but they have to back it up with a credible source. This gets pretty competitive, so the students really hold each other accountable.


Here are some important questions that we discussed after completing this project:

Goat image from Microsoft clip art

Goat image from Microsoft clip art

  1. Why do we lose calories when we feed them to livestock?
  2. What is the “best” crop? (calories vs. nutrients)
  3. Should we be putting plant calories into livestock?
  4. What are the pros and cons of having livestock?
  5. What would be the “best” livestock? (For example, for many reasons crickets are much more energy efficient than cows.)
  6. What does this make believe scenario have to do with the real world?

Tips and Suggestions

I suggest you have a running list of “rules” that you as a group decide upon throughout the project. For instance, someone will probably ask if it’s okay to do a rooftop garden. Whatever you decide, you should keep documentation of the “rules” your class makes. The students get pretty competitive and this is helpful.

To simplify our model, we assumed a lot. 1) People only need calories to survive, not certain nutrients. 2) We have sufficient water, fertilizer, and everything else needed to grow the crops. 3) We can store crops up to one year, and there is no limit to the type of crops that can be planted due to climate, etc. 4) Animals can only eat the part of the plant that humans eat. 5) All animals reproduce each year. 6) We eat the entire weight of the animal in meat. And more. But, these assumptions lead to fantastic discussions! I have students write about them for part of the end paper. They are also great opportunities for extensions.

Even with all of the assumptions and simplifications, the students were really able to “get it” in terms of energy transfer and the 10% rule.

If you’d like a more detailed description or have any questions, please e-mail me. jesirhodes@gmail.com

I know KELLY KLUTHE has some cool stuff to share! Tag, you’re it!

TBT: Fastplant Growing Tips

Editor’s Note: So, Brad Williamson is a pretty big influence on science educators here in Kansas and across the country. Here is a post he originally put on the BioBlog in August 2013. Fastplants are a good way to teach genetics, botany, evolution, ecology… maybe it would be easier to say they are a very robust model organism. 🙂   Enjoy, and let us know if you plan on using Fastplants this school year!

Since many AP Biology teachers are trying to grow Fastplants for the first time, I thought I’d do a few blog posts that follow a generation of Fastplants in my lab.  When I was in the high school classroom I always had a surplus of seed stock available because I was always growing the plants.  Now,  I just grow them occassionally because I think it is fun and also to provide starter seed stock for the new biology teachers that graduate from our UKanTeach program.  Back in July I was fortunate to travel up to the University of Wisconsin for another Fastplant workshop.  Paul and Hedi had Fastplants growing in a number of different types of containers

but I was particularly interested in the deli/discovery cup growing systems because they are very close the the technique I used to use in my classes back when film canisters were available.

The water reservoir (the deli container) can be used to also deliver soluble fertilizer so there is minimal care needed.  These containers are a bit small for weekends so I chose to use 16 oz. containers.

I returned from Wisconsin with some new ideas to try out as well as some seed.  Note that I brought the seed back stuck in tape.  We used the tape to pick the seed up and folded it back over itself to seal the seed in after making a couple of folded over tabs on the end.

You’ll find a description of this technique in several of the resources on the Fastplant website:  http://www.fastplants.org/pdf/growing_instructions.pdf

In the mean time one of my former students asked me about growing Fastplants so I decided to go out and get some more current cost estimates for supplies.  Assuming you have a light source but otherwise are starting from scratch here is what I found.

Soluble fertilizer from a local garden store:  20-20-20 with micronutrients

Artificial seed starter mix soil:

or a larger bag:

Deli Growing containers from Party America or Party City:

along with lids:

The portion cups from Party America cost about $3.50 per 100 1.25 oz. cups.  I already had quite a bit of yellow braided nylon mason twine from Home Depot so I don’t have a cost for that.  The neat thing about this system is that the individual cups can be moved about and that module based system is pretty easy to manage in a classroom.  I also purchased a can of Flat Black Spray Paint (one coat) that I used to paint the deli containers and lids to hopefully reduce algae growth in the water reservoirs.

I marked and cut 1 and 3/8 inch diameter holes in the lids to hold the cups.  I purchased a 1 and 3/8 inch spade bit to do this for about $5.  The holes are cut very carefully and slowly by running the drill backwards or counterclockwise.  In that way the bit just kind of scratches its way through the thin plastic of the lid.  Going in the forward or clockwise direction will likely lead to different levels of disaster—the bit is not designed to cut into such thin material in the forward direction.  If you drill that way you’ll just tear up the lid and likely not produce any holes that will work.

Marking the hole locations with a paper template.

Carefully drilling in reverse to cut the holes:

I added 250 ml of dilute fertilizer solution to each deli system.  I mixed the 1 measure (a full bottle cap from a 20 oz. soda bottle) fertilizer in 1 liter of water and then diluted that stock solution 1 part stock solution to 7 parts water.   I also drilled 1/8 inch holes in the bottom of the 1.25 oz. portion cups, added a 6 inch length of twine to serve as a wick, added moist soil mix to the cups to get ready to plant.

You can see the bluish fertilizer in the systems to the left and the wicks extending out of the cups on the right.  I moisten the soil so that I can work with it in a gallon plastic bag by squeezing water into it.  You can see the bag at the top of the tray.  Before I place a cup of soil into one of the systems I first make sure that the wicking system is working.  To do that I gently poured water from the pitcher in one of the cups until water was dripping from the wick.  This ensures that the soil is moist as well.  Once the water was dripping from the wick I transferred the cup to one of the growing systems.

I then planted 4-6 seeds in each cup (I will trim this back to only two plants in each cup in about a week).  The seeds were simply dropped onto the surface of the moist soil.  They are not “planted” beneath the surface.

At this point I added a little bit of horticultural vermiculite to the surface of each cup.  I got this tip from Paul W.   You could sprinkle a little bit of soil at this point but vermiculite helps the germinating plant to escape its seed coat.  I did not include the vermiculite in the costs above but I imagine it is around $8 for a small bag that will last for years of classroom plantings.

The systems then went under the lights.  Notice how close I have positioned the lights for now.

Day 0.

Day 1:  No apparent change:

Day 2:  We have germination

Day 3:  Most of the plants have germinated.  The cotyledons are expanding.

I’ll continue to report on this round of growing Fastplants.


Reason #47 to Talk Soils with your Students

KABT816VennDiag.001If you are a person that falls into the center of a Venn Diagram with one circle representing RadioLab listeners and the other representing people that watched/attended the 2015 KABT Fall Meeting, you might have already made this connection. If you are not if you fit into this Venn Diagram at all, please do yourself a favor and check out this, and this, and this, and also this… I can wait.

Are you back? Pretty neat, right?

Radiolab’s latest podcast is one of their best (soils bias showing here a bit) and deals with the importance of fungal communities to plant productivity and ecosystem health. It isn’t particularly long, so I intend to use it as homework, or an activity for a rainy day in case one of my sections somehow gets way ahead of the others. #WoodWideWeb 😂

At our 2015 Fall Conference, we had presentations from KU researchers Dr. Ben Sikes and Dr. Peggy Schultz that really lit a fire under the people in attendance. Their research deals with some of the myriad ecological applications of fungi in prairie ecosystems.  I think you will notice some crossover here, which is pretty cool. Dr. Schultz’s talk is especially linked to the information in the podcast, and does a good job of touching on the science of how the AMF (mycorrhizae) function. Here is video from their talks.

Dr. Peggy Schultz (Kansas Biological Survey) beginning at 00:42:15.

Dr. Ben Sikes (Kansas Biological Survey)

Where might this fit into your classes? Is this information an addition to your ecology unit? Or do you work it in when you talk fungi and/or classification? If you have more time to devote to soils and fungal-plant mutualism (environment science and field biology classes?), you might contact the two KU researchers; both labs do a really great job of outreach to classroom teachers and students. You can find their contact information here.

Figure courtesy Dr. Dan Carter http://sewrpc.academia.edu/DanielCarter

Effect of AMF on Growth in Grass Species. Figure courtesy Dr. Dan Carter http://sewrpc.academia.edu/DanielCarter

Not sure where this fits into your class, but want to try? Post a question in the comments or in our Facebook group and let’s have the Hivemind work on it! And let us know if you picked up on the hidden reference to the RadioLab podcast.


TBT: Teaching Genetics in the 21st Century

Editor’s Note: Though not planned this way, let’s make it two in a row for Eric Kessler. He originally posted this in July 2012. With many of us starting to plan for the next school year, now is the perfect time for an article like Dr. Redfield’s. You may not agree with everything therein, but it is definitely thought-provoking. After reading the PLoS article, let us know what you think in the comments and we’ll get this conversation started. -AMI

Read this PLoS article

And the developing comments.