SimBio blogs

Learning to use ecological models

Eli_Meir — Thu, 19 Jan 2012 07:34:49 -0700

Last week we announced Patchy Prairies, our latest SimBio Virtual Lab. Those of you who used our Corridors, Stepping Stones, and Butterflies lab in EcoBeaker will recognize the storyline in Patchy Prairies - you have money to restore habitat for an endangered butterfly in Oregon. Where should you put it? What we didn't elaborate on in our brief announcement was how the new version is an experiment in teaching students how models are really used in ecology.

As in the original, part of Patchy Prairies asks students to try different restoration landscapes to see which are best at boosting the butterfly population. That makes for a very engaging lab as students draw different maps and root for the butterflies to survive (it's been one of our more popular labs in ecology and conservation courses). But we didn't think students were making enough connections between the lab and how conservation biologists actually use models.

In the new Patchy Prairies, we keep the same goal (save the butterflies through habitat restoration) but put the modeling front and center. Our Automator gives students a simple way to run models multiple times and check whether results change as they manipulate different parameters. Rather than simply asking "what habitat configuration is best?", we also let them ask "what butterfly behavior is most important for us to study further in order to pick the best configuration?". It's a higher-level question, but we hope we've managed to pose it in a way that beginning ecology students can grapple with. For me, this is a re-expression of one of the original philosophies behind EcoBeaker - giving non-programming students the ability to play with ecological models.

Patchy Prairies is in beta this spring. We'd love for you to try it out and send us your feedback. Just get in touch and we'll be happy to give you access.

Education and equity - which goal comes first?

Eli_Meir — Mon, 09 Jan 2012 20:06:37 -0700

A tiny northern European country half above the arctic circle has become the latest fad in the what-should-we-do-to-fix-American-schools conversation. The country of Finland achieved this status by consistently scoring as one of the top countries on the PISA, an international test of educational attainment.

Unlike some of the other top scoring countries, though, Finland doesn't get there by drilling students in the basics for many extra hours a day. There are no after school and weekend tutoring sessions, no reams of standards and standardized testing, no competition between schools (and no private schools). According to an interesting if a little starry-eyed recent documentary exploring Finland's education system (The Finland Phenomenon), the students don't even do much homework. Yet despite going against the grain compared to the direction the U.S. and many other countries have headed, Finland students seem to be among the best at just the kinds of standardized tests that the Fins don't even use for themselves. All indications are they have found an alternative path for K-12 education that works really well, and we might have something to learn from them.

One reason that the film and other commentators have given for Finland's educational success is the professional respect accorded teachers. Being a Finnish teacher is apparently a highly coveted job, so their education schools can select only the best students. This is in contrast to the U.S. where teaching is too often a fallback profession for college students who have not found a passion for something else. After training these future teachers to a high standard, the Finnish system appears to give them free reign to teach rather than constricting them to following standards and judging them on test results. I think this is the same psychology that we try to use with our labs at SimBio - if you let people (be it students doing an open-ended virtual lab or professionals doing their job) have room to explore and carry out their own ideas, they will often be more inspired, try harder, and go farther.

What prompted me to write this post, though, was an article I recently read in The Atlantic that posited another reason why Finland's system is so good. Relying heavily on interviews with Pasi Sahlberg from the Finnish Ministry of Education, who has just written a new book on Finland's schools, the article claims that underlying Finnish success is a goal of equality. Finland decided that giving all students an equal education, and using that to even out social inequalities in the country, was a bedrock principle on which they would reform their education system. The author speculates that this equity principle fostered much of the success of the system they developed. To me this is a really intriguing (and admirable) goal for an education system and certainly a contrast with the U.S. explicit goal of improving educational quality as measured on tests, which, paradoxically, seems not to be working at all.

Fun evolution stories

Eli_Meir — Wed, 31 Aug 2011 13:52:16 -0600

One of the joys of going to meetings is browsing new science books in the exhibit hall. At the ESA meeting earlier this month, one book I found was In The Light of Evolution, which I ended up reading the whole way home and am still picking up many nights. Edited by the evolutionary biologist Jonathan Losos, the book features a wide-ranging collection of biological stories, each tinged with evolutionary thinking. The chapters are written by the people who helped discover each story, and it's obvious that a lot of effort went into making the writing very accessible.

Among my favorites was a chapter on what we know about humans evolving to stand on two legs, by Daniel Lieberman, and how this is related to our prodigious ability to sweat (I never realized sweating was such an unusual trait). Another nice story by David Reznick talks about his studies on how guppy life histories change in different streams - perhaps I like this one because it would make a great complementary reading to our How The Guppy Got It's Spots lab. I also really enjoyed reading about co-evolution between garter snakes and the super poisonous rough skin newts by Edmund Brodie III, complete with descriptions of how to make snakes barf up their last meal (a study we also discuss in our Predation, Herbivory, and Parasitism chapter - though I didn't know before about the amusing data gathering techniques). And there's many more, most of which are similarly engaging.

If you need some cool, well written evolution stories for one of your classes, I'd definitely recommend looking over In the Light of Evolution.

New Respect for Opossums

Jon_Herron — Tue, 09 Aug 2011 02:37:17 -0600

Driving home just now through my neighborhood, I encountered an opossum crossing the road. I try not to think or speak ill of any creature (except maybe some pathogens I've known only too well), but it's hard to avoid the impression that opossums are ugly, stupid, and slow.

I'm not saying they don't clean up nice for photos...

...but seriously, have you met one?

Imagine my surprise when I learned from a recent paper in PLoS ONE that opossums eat pitvipers. Rattlesnakes and lanceheads. Maybe you knew this already. According to the authors, Sharon Jansa and Robert Voss, the behavior was first described by Spanish naturalist Félix de Azara in 1802. But it was news to me. Here's Jansa and Voss's account:

Opossums that prey on pitvipers appear to exhibit no behavioral precautions while subduing these dangerous snakes, and they are often bitten in the process.

How can they do this? They're immune to snakes' venom. Jansa and Voss show that resistance to pitviper venom is associated with amino acid substitutions in von Willebrand Factor, a protein involved in blood clotting that is targeted by the venom. And they present evidence that the opossums' von Willebrand Factor gene is evolving rapidly enough to imply an ongoing arms race with the pitvipers. An arms race in which the opossums are the predators and the snakes are prey.

Those are some extreme marsupials.

Sources:

The photo of Didelphis virginiana is from Wikimedia Commons.

The paper is Jansa S. A., and R. S. Voss. 2011. Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers. PLoS ONE 6: e20997.

Sound Science: Simulating at Blind Youth Slam

Eli_Meir — Wed, 03 Aug 2011 07:19:31 -0600

One problem with biology labs in general, including our own virtual labs, is that students who can't see are excluded from using them. That's a shame, and something we've wanted to find a way around for a long time. That's how I found myself in Baltimore a couple weeks ago, helping our vice-president Ellie Steinberg run workshops for the National Federation of the Blind's Youth Slam.

A week-long summer program organized by the Jernigan Institute, Youth Slam this year was on the Towson State campus in Baltimore, with workshops and classes designed for blind and low-vision high school students who are interested in science. Other than the ubiquitous canes, we met the same range of mellow, excited, and boisterous kids you'd find at any summer camp. The goal we set our sessions was for the students to be able to navigate through our prototype “accessible” version of our most popular virtual biology lab, Isle Royale, to conduct a series of simulated experiments, and in the process, learn something about population growth and predator-prey dynamics.

Going into this project, which is funded by the National Science Foundation, we figured there must be examples of accessible scientific displays we could use as the basis for our work. There are, in fact, nice tools for making static graphs accessible - specialized tactile printers and touch-pad interfaces, for example, that let a blind person interpret graphs using touch and sound. But these don't work well if the graphs are constantly changing over time. In previous projects we used the pitch of a sound to indicate the height of a line on a graph, and a few other software packages do that as well. But to learn about predator-prey dynamics, you have to compare changes over time for multiple interacting species. Apparently, no readily available software package let's you listen to multiple variables at once.

So, we decided to try it. Working into the wee hours the night before our workshops, we gave each species a different timbre - flute for the wolves, viola for the moose, harmonica for grass, and so on. The students first focused only on the moose population. They easily distinguished linear versus exponential growth curves, and could hear the moose population skyrocketing initially and then crashing back down to a carrying capacity. So far so good. Next we challenged the students to figure out which of the three plant species the moose were eating. Listening to how the plant populations changed over time in comparison to the moose population, they figured this out as well. Then we reached the part of the lab where they add wolves, and had to compare population dynamics of up to five species to figure out what was going on.

Having multiple voices worked! It was really exciting to see. Using a special graph interface we built, many of the students figured out the population cycling, and the phase differences between species. Not only that, they were jazzed - some commented that it was the first time in their lives they had been able to really explore data on a graph. Afterwards, some were telling us about all the dumb stuff teachers came up with to keep them occupied in normal science labs - apparently even a prototype stripped-down virtual lab was miles better.

Simulation labs are challenging to make accessible because they are so visual, but this small experiment shows that with some thought and effort, it's possible to go a long ways towards accessibility. Our attempt is still quite rough around the edges and we have a lot of work left on the details, but we're now very hopeful that in the near future, some judicious use of sound will let a whole new group of students take advantage of active science learning through virtual labs.

Labs, labs, glorious biology labs

Eli_Meir — Wed, 04 May 2011 07:07:11 -0600

Last week I wrote about the new interactive chapters and SimUText features coming for this fall. We haven't neglected our labs this year either. Here's what's new in SimBio Virtual Labs for fall 2011.

Many of you have been helping out in our genetics research study by using the Mendelian Pigs lab this spring. As part of an NSF-funded study, we're testing a hypothesis for how to help students understand the Hardy-Weinberg equation and other population genetics concepts. While the study will continue in the fall with a modified version of Mendelian Pigs, we'll also be releasing the lab itself. It covers both Mendelian and population genetics and how those relate to each other, at a level suitable for an introductory class.

As part of the same grant, we've also been working on a new lab to help students with genetic drift. Still unnamed, the lab focuses on a conservation story around an endangered species of ferret and culminates with students designing a breeding and reintroduction strategy that preserves genetic diversity. We expect a beta of this lab to be out in early fall.

We've been upgrading our older EcoBeaker labs to our new SimBio Virtual Labs system all through the year, and taking the opportunity to improve them as we go. Some of you have already been using our new Niche Wars lab (fondly remembered by many as the bunny lab) where students must get different "species" of bunnies to coexist, exploring niches and competitive exclusion along the way as well diving into how agent-based models work.

Also out this spring is our new Finches and Evolution lab, an update of our older EcoBeaker lab called Islands and Selection. Using Darwin's finches as a case study, the lab explores how selection acts on quantitative traits, trait correlation, and possible ways of getting incipient speciation.

This spring, we've just finished two additional upgrades. Leibig's Barrel is a new version of our popular Limiting Nutrients lab. After exploring how nutrients can limit growth in an algal system, and how the "limiting" nutrient is always relative to the concentrations of other nutrients, students then use single species growth to predict competitive outcomes between multiple species under different conditions.

Top-Down Control updates our former Trophic Cascades lab. It recreates the famous Brooks and Dodson experiments where they added fish to a fishless lake and observed the trophic cascade that followed. Students are given a variety of tools and must do experiments to explain that cascade. This is a very open-ended lab, good for giving students experience with conducting their own experiments.

A final lab we're working on this summer is Corridors, Stepping Stones, and Butterflies lab. One of our most popular EcoBeaker labs, it uses the plight of the Fender's Blue butterfly in western Oregon to explore landscape effects on population survival, and how models can be used to help in conservation and restoration ecology. We expect the new version to be ready in early fall.

It's been a busy year, as you can see, but exciting to be able to offer so many new ecology and evolution labs. Hope you enjoy using them. As always, we are very open to suggestions. If there's an area of biology where you would love to have a virtual lab for your classes, please let me know.

Coming In SimUText This Fall

Eli_Meir — Wed, 27 Apr 2011 13:55:30 -0600

We have a lot of new chapters, labs, and program features in the works for fall 2011, and I'm excited to share them with you after another year of hard work by everyone at SimBio. Since there is so much new, I am going to split it into two blog posts. This week, I'll share what is coming for SimUText Ecology, and next week, I'll write about our new labs.

Let me start with the new chapters we're working on. One of our earlier outlines in developing SimUText was for a Decomposition chapter, and we're now finishing that up. It uses two storylines, one about a change in tree species at the Coweeta LTER site, and a second about forsenics, to help students explore the decomposition triangle of litter quality, temperature, and moisture.

Our second new chapter is on Biogeography and Conservation. Some of you have seen the single section of that chapter we currently have available. We are fleshing this out into a full four-section chapter that will cover biodiversity measurements, global patterns in biodiversity, island biogeography, historical biogeography, as well as biomes and the associated global weather patterns. We're working with folks from The Nature Conservancy among others to get associated real-world conservation examples. While slightly delayed, we expect this chapter by September 2011.

In addition to new chapters, we have several major upgrades. Physiological Ecology went through two major revisions, the first as we officially released it this winter (it was in beta last fall), and another this spring as we fine-tune presentation of more complex ideas like transpiration and the heat balance equation. Population Growth is also going through a major overhaul. This was the first interactive chapter we ever wrote, and is showing it's age. A major addition is a new section on metapopulations. We've also added material on time-lags in population growth, and reworked some of the mathematical sections as we learn what helps students through these. Finally, Competition had a big revision based on feedback, including an even nicer section on Lotka-Volterra competition models.

In parallel with chapter upgrades, we've been busy improving the underlying software. You'll see a dramatic change in the look and feel of chapters. The navigation is much improved with fly-out menus letting you jump around more easily, and options to see the full glossary, full bibliography, or all the formulas in a chapter. These make information more accessible and should aid students in studying for exams. We will also have beta-versions of new note-taking and highlighting tools.

Our Instructor Portal is getting some love too. The biggest addition is a Statistics Panel where you can sort questions to zero in on those where students are doing well or poorly. We've also added flexibility in the score export spreadsheet, and made changes under the hood that will keep everything responsive as the number of students continues to grow. Finally, we are working on making the powerpoint slides that complement the chapters more useful.

That's a lot of new stuff. It feels really good to have so many of you using SimUText Ecology again in 2011/12 as a replacement or supplement for the text in your classes. We don't yet have samples showing the new features, but if you would like a tour, I or one of the other authors would be happy to do a demo for you. Just let us know.

Next week - the new labs.

College for all? What's the point?

Eli_Meir — Fri, 08 Apr 2011 07:16:02 -0600

A bachelors, masters, or PhD is viewed as a ticket towards a satisfying and stable career and becoming a well-rounded citizen. Certainly college graduates make a lot more money than those without that degree. Yet an increasing number of articles and blogs are starting to question whether "College for all" and "You should go to graduate school" are really good mottos for our society.

Lot's of students who go to college now are not prepared, not really interested, and don't graduate. Those students end up with tuition debt but don't necessarily earn more than their friends who got only a high school degree or an occupational certificate like electrician or dental hygienist. Such observations are driving a number of high-profile articles such as this one from the Harvard education school to question whether we should really be pushing all our kids to go to college. It's a sentiment that's been growing over the past few years and although I don't like that it verges on giving up on a lot of students, I'm starting to be convinced the view has merit. Many of the skills we teach in college (and high school) nowadays are only useful for a select group of jobs, and the range is shrinking as standardized testing and large class sizes narrow the skills being taught.

Countering this is the move in college science teaching towards emphasizing thinking skills, such as SimBio does with our virtual labs. But even at the graduate level, where one would expect such broader thinking skills to predominate, a recent set of blog commentary here and here points out the learning is often quite narrow. In many biomedical labs, for instance, PhD students perfect techniques of dissection, microscopy, working with specialized instruments, and other skills that really don't apply outside a narrow band of research for which there are less and less jobs per qualified applicant. And although I am proud of our own virtual labs for teaching students how to discover fundamental biological concepts and ask and answer questions for themselves, it's hard to say whether even those broader thinking skills apply to large swathes of life. I've gotten pretty good (well, not awful) at fixing the plumbing on my boat (not through any innate desire to learn this, let me assure you). Has my training as a scientist helped me there? Or is it a completely separate sphere of learning that I've had to pick up? I like to think my research background lowered my plumbing learning curve, but I'm not honestly sure.

So I'm starting to appreciate the line of thinking that says some students should not be pushed towards a standard college degree, and there should be more emphasis given to other possible career paths. Nevertheless, I'm still not ready to give up on trying to offer all kids the opportunity for a more general education. We just have to broaden what we mean by general education to include a more diverse set of skills and learning styles. Much of the work in the biology education community is aimed at doing just that - the aforementioned shift towards inquiry learning and thinking skills, incorporating more writing, presenting, and collaborative projects, offering early research experiences which allow students to tinker hands-on, and so on. At the graduate and postdoc level, there is a growing realization that classes and opportunities to learn to teach are important, as are thinking early about possible careers other than becoming a clone of your advisor. All of these moves still won't help someone become a plumber, but they do apply to a much broader range of jobs, and life, than simply remembering the stages of mitosis.

In this context, I can't help but mention a project from my colleagues at MIT who have just released a new science game for middle-schoolers. It's called Vanished. It's running for 8 weeks, from beginning of April through the end of May. It's a big sciencey collaborative puzzle that thousands of kids across the country are working together to solve (involving lots of those skills and motivation that's missing from our traditional science curriculum). If you have a middle school kid in your life who you want to experience a different science education possibility, have them check it out.

Climate Change teaching with the IPCC's Steve Running

Eli_Meir — Tue, 01 Mar 2011 08:30:12 -0700

One of the great things about writing our SimBio interactive chapters is the chance to talk with a lot of interesting scientists. Among the reviewers of our Climate Change chapter was Steve Running, a climatologist who was part of the IPCC group that received the Nobel prize a couple years ago. His work with the IPCC and increased profile after getting the Nobel has led to a lot of invitations to speak about climate science to both academic and general audiences. Dr. Running recently agreed to sit down and share with us his thoughts on climate science concepts that are difficult to convey and how he approaches them in his talks.

He has some interesting thoughts on how to present climate modeling as based on a long scientific history. If you address climate change in your classes, you can read the summary of our interview here:

Teaching climate science interview with Dr. Steve Running.

I'm biased of course, but I think our lead author John Roach did a super job leading students through an understanding of climate and climate models, the data that earth's climate is changing, and possible ecological consequences in our own Climate Change chapter. In case you haven't seen it yet, here's a page with instructions on how you can try our Climate Change chapter yourself.

Enjoy.

New Release: Finches and Evolution

Eli_Meir — Wed, 23 Feb 2011 07:43:07 -0700

I'm excited to announce that we've finished a new SimBio Virtual Lab called Finches and Evolution. This major update to our old Islands and Selection lab uses the classic study system of beak depth and width of Darwin's Finches to introduce quantitative population genetics. It's loosely based on the work of the Grants and their students in the Galapagos, as nicely summarized in the famous book Beak of the Finch.

In the SimBio lab, students investigate selection on quantitative traits, how selection is affected by genetic diversity, and the effects of correlation between traits. Then in the final experiments, students are challenged to get a single population of finches to diverge into two sub-populations adapted to different environments. It's pretty fun - once you get the conditions right, you see incipient speciation happening right there on the screen.

If I've piqued your interest, we'd love for you to take a peek at Finches and Evolution. To make that easy, I've set up a temporary open-access login on our SimUText system. Just go to the following web page for instructions:

http://simbio.com/promos/try-finches

If you'd like to try the lab this spring, get in touch, and we can set up your class with the lab in exchange for some feedback.

Enjoy!