A scaffolded Biology assignment 2

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Arrangement of Specimens by Hyppolite Bayard. Digital image courtesy of the Getty’s Open Content Program.

Tomorrow has become 2 days later…but here is the assignment. The general outline is:

  1. Students select a topic. This can go different ways. For a non-majors general biology class, I have asked them to choose a topic that interests them. I provide a list of examples, but encourage them to propose their own after discussing it with me. Thanks to that, I recently learned a lot about deer antlers (courtesy of a student who likes hunting) and have been given insight about opinions about GMOs (that would be another posting). The idea at the non-majors level is to practice biology literacy. At higher level courses the topics become more specific as the idea is to explore deeper. So for example, in a majors bio class I would give them a list of genetic disorders to choose from. By providing clear gene and protein targets, they can explore them much more in detail. In microbiology the idea is to study some kind of microbe at the structural and functional level.
  2. An important part of the process is defining what students are going to post about in each iteration. This is indeed, the hardest part. We want students to peel away layer after layer of their topic, instead of just doing a mini-wikipedia like summary. So I have found important for students to make an outline of their future postings/reports. For a general bio topic, it can go like this: gene => protein=> physiological function => population level (this can be inheritance pattern, epidemiology, economical impact etc). For a microbiology topic it can be: microbe’s structure => microbe’s function => population/societal impact.
  3. Then come the analysis at different levels. Depending on the class, more or less information and details will be required. I try to have students visit databases, and gather data. Even if they don’t know what to do with a DNA sequence or a Jmol structure, it is often an eye-opener for them that all that information is available online.
  4. Feedback, feedback, feedback. It is a lot of work, and that is why grading rubrics are useful. I tend to move in grading from formative to summative. In the beginning, the main criterion for grading is if they actually submit the information required and follow instructions. With more practice, I expect them to be more specific and actually process the information.
  5. Final report: at the end of the process, students are to summarize their research in one piece of material. I often like it to be a poster, as combining text and graphic information in an efficient way is a useful skill. When at the Yale SWI workshop, one colleague share his way of practicing effective poster skills with his students: he would pick up a bunch of poster printouts from conferences and would give them for students to analyze. Which structure or format seemed the most effective in transmitting the message? I have tried other formats, from powerpoint presentations to wiki pages. However, I have found that posters have such a stringent space limitation that students do need to focus on the key information and how to best convey their messages. Oral presentations are another great way to practice communication skills. Here, following time limits is critical.
  6. Peer feedback. Interactions between students are invaluable. However, if left spontaneous, comments on these kind of projects will be usually rather superficial. I have found that the peer evaluation part of any of these processes has to be scripted if it is to be meaningful. In my latest iteration of one of these projects, I had to spell out that the comment had to include 3 parts:
    • positive feedback about something that the observer liked
    • a question
    • a suggestion

And this is all for now. Heading to the San Bernardino mountains tomorrow for the long weekend. Should be cooler up there. Happy Labor Day for those in the US!

A scaffolded assignment for biology courses 1

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Barthel Beham, Study of three skulls: different views of the same subject, a work in progress. Digital image courtesy of the Getty’s Open Content Program.

For the past couple of years I have been polishing a kind of formative assessment that works very well for biology classes, especially general biology. It is not my invention of course: in my school’s MS Bio program students analyze their selected thesis topics from a variety of point of views (molecular, cellular, organismal) as they move through the different courses, and I was also much inspired by Prof. Campbell’s approach to teaching molecular biology through the “Your favorite…” assignments.

Most biologists would recognize this approach as attractive, as it appeals to the basic core concepts in biology, including the levels of complexity of living matter, the relationship structure-function, and the notion of any scientific topic being inherently complex. Deconstructing a topic to its simpler components to understand it, and then putting it together again in a larger perspective is what we do all the time as scientists. Applying the process to a topic that  students find personally interesting ensures they will be more engaged. In summary, a win-win situation.

As most things, the devil is in the details.

Lately I have been thinking a lot about my teaching. Between the informal mentoring by my education colleagues and several science education projects, it has become now more of a routine to think along the lines of “what do I want my students be able to do” and “what are the activities through which students can practice.” During the Coursera Gamification course I learned how good games aim at the edge between boring and challenging, and how the learning curve should be gradual to avoid losing players giving up in frustration. I lived it during the annotation practices of the GEP workshop: I consciously chose an easy project to start with so I could have a positive experience of being able to finish and then move to a harder one. The learning curve was still steep, but I had some sense of accomplishment, while some of my colleagues who chose complex genes with multiple isoforms sat through both days pulling their hairs.

And then of course there is also the issue of guidance. Discovery-based instruction is outed as the best way to teach science and I agree. However, we cannot really expect students to grasp the complexities of the research process by themselves, especially at the undergrad level.

When I started implementing these types of assignments, I assumed (incorrectly) that students would see right away the purpose of peeling away the layers of complexity of a biological topic, and would be able to analyze it with discipline, to finally put it back together. At certain levels, some students could, but most struggled and delivered “generic” reports, often obviously copied from wikipedia in discordant chunks.

With time and practice, I have gotten better at introducing the assignment, walking students through the process, and providing more detailed instructions. During the latest iteration, in a non-majors biology course, I developed highly detailed grading rubrics so students had no doubts about what was being asked for them. I personally dislike grading rubrics, as they are easy to game once you know how they work. On the other hand, especially in online courses, they are helpful to guide students as to expectations.

And then came the epiphany.

A student was writing about GMOs. We are talking a non-majors general biology course. It was the posting that should have tackled the molecular aspect of her topic, so I advised her to focus on one or two GMOs and look at the particular molecule that was being introduced and what it did. She mentioned in passing that the genes introduce resistance to insects or improve culture conditions, but the rest of her writing was a passionated diatribe against GMOs. And she did not meet the word count requirement.

I groaned in frustration. Didn’t I painstakingly break down point by point what I was looking for? Didn’t I post clearly that there was a minimum of 750 words? I huffed and puffed and moved on to the next posting, after giving her a hefty markdown.

Then came the squeaky clean postings. The ones that followed point by point what I was looking for in the instructions. With impeccable wording. No obvious plagiarism, but if you know how to do it you can evade the detectors. After happily assigning high scores to a bunch of them, I started to feel concerned, and went back to the first student’s writing. In comparison to the other postings, her writing was passionate and hers. She wrote to convey a message that was personally important for her, and I could see a clear space for improvement in that assignment. Improvement not only for better analysis, but also for a better knowledge in an aspect of her life that was important for her.

Just that day I had found this posting of “Dean Dad” Matt Reed very relevant to this train of thought, where he distinguishes two types of writing errors: “errors of laziness or ignorance, and errors of attempted growth.”

So what was my epiphany? That grading rubrics are useful for those students who know how to use grading rubrics, and will probably result in uniformly acceptable work with minimum attempted growth. But in other cases, one needs to be careful in deciding if this is just not paying attention/being lazy, or if this is somebody who needs practice in how to approach a complex topic. I am curious about the next posting.

And this is for today- tomorrow I will describe a bit more how I approach this kind of assignments and share some of the experiences (good and bad) along the way.

Dear readers, please share if you use this kind of assignments, and what is your view about grading rubrics!

Microbial updates

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This has been a pretty hectic week, and with lots of food for thought. The situation in the world concerns me, and also other issues of the bigger picture. But today I will focus on updates on bugs. Taking care of microbes growing has  a zen-like quality to it. Call me old-fashioned, but waiting for a hot loop to cool is relaxing.

One of the bugs I brought from Yale, a perky Pseudomonas, has proved to be a funky one. Last week I strode into the lab and decided to try everything available in the fridge, and inoculated all kinds of media to get more information. Results came out along the expected ways (negative fermentation and MR-VP among others), but the nitrate was negative. The sequence had been pointing at a weird fish-killing Pseudomonas, but  P.plecoglossicida is nitrate positive. My bug did not seem to be fluorescent under UV light, so P. fluorescens seemed to be out of question, but it is nitrate negative, so I inoculated a couple of gelatin deeps and am waiting for the results, gelatinase production being one of the distinguishing features. I have been around labs enough to not get too excited about weird stuff, and I just cannot believe that the soil at Yale University is harboring some kind of special bug. But at the end that is not so important…it is the antibiotic production that matters. So I am also repeating the spread/patch plate against four bugs, including E. coli & P. aeruginosa. After that, if things repeat, then I will have to make some decisions about what to do next.

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West Coast & East Coast kombucha. Just refilled the East Coast one, that’s why it is in the bottom.

As for kombucha, as they say, no news is good news. It has been growing placidly in the corner, by now in its 3rd of 4th tapping. The first ones had 1/2 cup of sugar per liter, and were very sweet in the beginning and very tart at the end. Then I halved the sugar amount, and the resulting drink was way mellower but also bland. I had started experimenting with diluting the strong concoction with fruit juices, which seems to produce a pleasant flavor. Another option is to add chia seeds, which give a nice chewy quality to the drink not to mention the added protein. I finally relented and bought a set of big jars for the cultures. The West Coast one has been steadily growing, and I can see it becoming equal to the Yale one, especially after today as I started to give away babies (tearing away a layer). Next stage will be experimenting with different teas and sources of sugars.

My next post will be about scaffolding assignments for a General Bio class. I had a kind of epiphany about grading rubrics the other day while banging my head in frustration because of students not following instructions. Stay tuned!

Small World Initiative: update on the babies

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The last day of the Small World Initiative at Yale my roommate and I walked down to the UPS store and shipped a few streak plates home. They were to arrive on a Thursday, the day I had to drive down to San Diego for a couple of meetings, and then I was leaving town on Friday. I asked the labtech to put the plates in the fridge.

I completely forgot that the little box was not labeled anything special, and as normal mail it was lovingly placed on my chair in the office. When I returned to campus the Tuesday after, I started opening the box with apprehension. “It will smell bad,” announced to the labtech as I started opening ziplock bags. “One of them seems to be a Pseudomonas.” Indeed, when the last bag was opened, the musky smell of earthiness surrounded us. However, the babies looked ok. The colonies were big and fat, but the plates were not overgrown.

That same day the 16s sequences had arrived via email, and after a quick Blast, the predictions based on Gram staining and colony morphology were confirmed. One was a Pseudomonas, the other a Bacillus.

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Inhibition zone on the E.coli spread plate around one of the colonies. Broken agar, my bad. Ugly lawn too.

With a microbiology course happening on campus, I looked for bad bugs to test, and found E.coli and Staph. aureus. I did a quick spread/patch plate with the 2 candidates. Today the Pseudomonas was showing a clear inhibition zone with E.coli, and a possible one with the Staph.

So this is exciting, although hardly earth-shattering. As an anthropocentric cell biologist (mea culpa, mea culpa) I knew a lot about antibiotic resistant nasty bugs such as P.aeruginosa, but I just realized there are a lots of other Pseudomonas in the soil that have to do with protection of plants from diseases. And those antibiotics are of the phenazine type. I just got started in the literature research, so I do not know much more, apologies.

That said, I do want to finish the SWI sequence, so next time it will be testing against the whole battery of ESKAPEs, and starting some traditional microbiology. Where is a Bergey’s when you need it?

I know it is not P. aeruginosa, as even when spread on a P agar it was not green. And I don’t think it is P. fluorescens because it does not fluoresce under UV light. Grateful for your advice as to how to proceed.

The other baby, the Bacillus, did not do squat to E.coli.

Still love them both. What do microbiologists say? “You get attached to your bugs.”

Amen to that!

Once a bum always a bum

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Image

View of the Coachella Valley from the air (last week’s flight home)

“We find after years of struggle that we do not take a trip; a trip takes us.”

I read John Steinbeck’s Travels with Charlie when I was in my teens. I found it fascinating, although at that time probably did not understand half of the very American references in the book. Upon re-reading it couple of years it struck me how valid many of his points still are.

And of course the paragraph about excitement of travel just hit home. This is exactly how I feel. I may complain about the stress of travels and time away from home, but in my heart of hearts, this is what I truly love to do.

I am writing this from a Starbucks along the I-10, as I drive East this Friday morning. I am teaching an online class, but I will have internet in the mornings and evenings, and I warned my students I won’t answer their emails within 5 minutes as I often do. My files reside in my Mac and in the cloud, accessible through a variety of ways.

What I am trying to say is, with the internet and the ease to stay connected, it is so much easier to travel these days. Even if teaching.

“When I was very young and the urge to be someplace else was on me, I was assured by mature people that maturity would this itch. When years described me as mature, the remedy prescribed was middle age.In middle age I was assured greater age would calm my fever and now that I am fifty-eight perhaps senility will do the job. Nothing has worked. Four hoarse blasts of a ships’s whistle still raise the hair on my neck and set my feet to tapping. The sound of a jet, an engine warming up, even the clopping of shod hooves on pavement brings on the ancient shudder, the dry mouth and vacant eye, the hot palms and the churn of stomach high up under the rib cage. In other words, once a bum always a bum. I fear this disease incurable. I set this matter down not to instruct others but to inform myself….A journey is a person in itself; no two are alike. And all plans, safeguards, policing, and coercion are fruitless. We find after years of struggle that we not take a trip; a trip takes us.”
― John SteinbeckTravels with Charley: In Search of America

Time to hit the road!

Ex-RNA in exosomes?

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Ex-RNA in exosomes?

It’s fun to read about things that were part of my life and kept going. Like exosomes. My little review from 2005 still gets a lot of hits due to the current popularity of exosomes. I follow what exosome people do in their Facebook page. It was a cool project to do. Lots of ultracentrifugations. Good times. What do you think about little vesicles and exosomes? Will they be the next diagnostic breakthrough?

Correcting course(s)

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I had seen it on the web some weeks ago and I covered my ears and sang “lalala.” But now that I have it in front of me, smiling smugly from the cover of Science magazine, I cannot ignore the giant Pandoravirus and its acolytes anymore.

Electron microscopy image of teh huge virus pandora

Enhanced transmission electron microscopy image of a “Pandoravirus” particle, from the cover of Science, July 19 2013.

Gosh, maybe Patrick Forterre is right after all, and we have to rewrite the three domains and invite viruses in? Consider them alive?

Please note that I am NOT a virus expert and I do not follow the field. However I did come across Forterre’s work quite a while ago, found it fascinating, and immediately tried to forget. Put my head in the sand. Because I have been there before, facing a group of non-majors who have to take a general biology class because they have to. And they find everything about biology complicated and tiresome, and they look at their textbooks as the source of all wisdom and then one does the science thing. The days I am more pacific I purr softly “There are new developments that question some aspects of this theory,” and may leave it there. Other days I may try to transmit the enthusiasm of new discoveries in science that challenge old paradigms. But few students share the joy, especially if they just got something and then I am ruining it for them.

It is interesting how the perception of changes is different when inside or outside the field. Inside a field, one is aware of the small changes due to minor discoveries that eventually may lead to a complete reevaluation of the existing knowledge. As an outsider to the virus field, I have been seeing only bits and pieces of discoveries, which now suddenly seem to be moving in a certain direction.

So I’ll wait and see. I still remember years ago, when the idea that the microbes living on our body could do something else that just try to invade us given the chance was novel and revolutionary. I went from the casual comment of “it seems like gut microbes can influence obesity” to the current discussion of microbiomes and their importance in health and disease. Maybe in a few years, those slides with the neat 3 domains will become something very different.

This reflection is coming of course from my non-majors general bio class that started yesterday. Even during our SWI discussions last week it was obvious that non-majors require an extra dose of fun and excitement in a science class to make it somehow memorable. That’s why I decided to go for the Phelan book, for several reasons: it reads easier, it has a great companion website, it has tons of real life examples and applications, it has lots of graphing examples and illustrations, it is cheaper than the one we used before, and overall it just seems to be more fitting the modern student. I am also drawing heavily from the ideas and rubrics of the Vision and Change report, which identifies a set of core concepts and skills that should be part of the undergraduate biology education.  It is nice to have some solid guidelines for the design of coursework.

Two glass containers containing kombucha

My kombucha cultures, day 3.

The kombucha mothers, by the way, have risen to the surface of the sugary tea, not completely yet, but exposing more “body” to the air. What a relief. Following the instructions, I have been tasting the drink daily, feeling a slight tanginess invading the sweetness of the original tea. It is very pleasant, and it is amazing how quickly the pH changes day after day. It should not take many more days to get to the right balance point.

Other than that, lots of catching up to do after the SWI week. My cultures should arrive tomorrow to campus, but will have to wait until next week in the fridge as I am out of town this weekend…again. Stay tuned!

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