Course Corrections

I've been teaching a course for the last 15+ years. I love this course because I conceived it and brought it to fruition. Since its inception, it has been modified a lot, primarily through interactions with the students who take the course. Initially it was a 'lecture' course, but from its inception it involved plenty of reading the scientific literature, discussion of said readings, and writing. 

One of the first major changes to the course was to make it writing intensive. In practice this did not change the course significantly, but did add an overt writing instruction component that was there but less explicit. It was about this time that I was much more active in writing to a general audience and actively engaged in science communication. These are still critically important to me, but my communication to a general audience have moved to the periphery as other commitments and responsibilities have taken over much more of my time. Regardless, my direct involvement in science communication impacted the changes occurring concomitant with the change to making the course writing intensive.

From here

While every year the course changes due to which scientific papers we use and to student interests/involvement, the fundamental structure has remained intact. This summer I am making some relatively significant changes to the course, at least in how it is delivered. The course is structured around a weekly schedule, where Monday is a didactic lecture in the organism we are discussing and relevant background related to the papers we are reading. Wednesday involves short student presentations on two primary research papers the entire class reads (the students address five specific questions related to the paper, but do not present the entire paper). Friday is a discussion related to specific aspects of the organism, papers from Wednesday, and student input from online responses.These discussion are completely open and are hard to prepare for as the discussions can go in many different directions. Regardless, the following Monday we move on to a different organism and set of papers.

Based on student feedback, I am making some significant changes. First, I am changing the M/W.F schedule to  a F/M/W schedule. Because students are reading two primary research papers for presentation/discussion, they have asked for the extra time the weekend provides to read and digest the material, as opposed to the Monday to Wednesday turn around time. This makes a lot of sense to me, so I am making this change for next semester, although it requires me to make some substantial changes to the course schedule. Second, students overwhelmingly indicate that the discussions occurring on Wednesday post-paper presentation and Friday facilitated their learning and engagement with the material. However they also noted it was difficult to see the link among organisms and topics. To be fair, there is no obvious link between these organisms/topics, other than all eukaryotes living today descended from a universal ancestral population. However, this is important and while I highlight similarities between what we were discussing in week 1 versus week 4, it occurs in passing during lecture or the discussions. So to more directly show the linkage, however disparate among organisms/topics, I am developing weekly worksheets for students to fill out asking questions like how does paper X discussed this week relate to topic Y from two weeks ago. Instead of trying to convince students of how analyses in one area can inform a distinct area, I am going to ask them to do that work in a directed way. In some cases there may be no clear links, but these higher level thinking exercises can be extremely informative to the students during discussion, but also to me (the instructor) to observe student perspectives/understanding. Third, I am developing at least one new type of writing assignment or at least making it overt that a writing assignment is distinct in style/approach than other assignments. Currently, students submit four essays that fall under the umbrella of 'essay exam'. Although these essays are completely distinct (one involves assessing a specific scientific paper, another a compare-contrast essay addressing a biological question in two distinct organisms), it appears (based on student feedback) that the distinction is not apparent. This coming semester, I am going to grade several distinct writing assignments that are completely independent...in other words do not fall under an umbrella of 'essay exams'. We already have another writing assignment, a blog post, that students do not report the same concerns with the 'essay exam' assignments even though grade associated with the blog post is slightly more than the individual 'essay exams'.

Basically, I want to facilitate student learning and embracement of, at least, some of the writing assignments. Why do I want do to this? There is much literature noting that writing facilitates learning (this is my personal experience as well).I'm not sure much more is needed to justify these approaches. However, science communication is sorely needed in society, especially societies where a significant population is more than willing to embrace non-scientific modes of thinking to justify policy decisions.

Will these changes improve student learning? I think so, but will need to make the adjustments and see how it works. The good things are these changes built on a solid foundation and are easy to alter if they do not appear to be working.

Daily routine

7:00 am coffeeeeeeeeeee
8:00 am more coffeeeeee
9:00 am more coffee maybe shower, maybe already showered. Regardless let's assume already showered

10:00 get to work/lab If I car pool this means getting dropped off at the St. Paul campus and taking the shuttle bus to near where I work, if I don't car pool this means parking next to my building and kicking the fuck out of the card reader until it decides I can get into my building.

10:05 open some doors and walk up several flights of stairs. Go to my office and unlock the door and drop my shit off.

10:10 go back through all the doors and down the stairs to get some more coffee. This requires going through key carded doors that don't require kicking the shit out of. In fact if I get near them with my card they work (Fuck you one outside door that is a total fuckstain!).

10:15 drop off coffee in the office and go to bathroom to wash hands. Yes I'm thinking about the shuttle bus handles and chairs as well as the door knobs I've touched getting to and from my office as well as getting my third coffee. Yes I use soap and get the paper towels ready ahead of time. Yes I use soap and use the paper towels to turn off the water. Yes I get more paper towels, which is ok my hands are still wet, to finish drying my hands and open the door. I use my foot to prop the door while I took the paper towels and exit the bathroom.

12:00 I don't know if this is the correct time, but I wash my hands because I've been in the lab doing science. (If I haven't been doing science in the lab, I wash my hands anyway because its time, and I want lunch.)

1:00 Go into the bathroom and wash my hands, I might use the facilities too as I've had 3+ cups of coffee.

3:00 Leave lab or office and wash hands, because its time and whether I realize it or not I've almost certainly done some things regrind door handles, stairs, countertops, or something lots of hands have touched.

5:00 At gym, use sanitizer. After running laps on track use sanitizer. Do some weight lifting with pulleys. Mucho sanitizer.

5:45 Don't touch face, you don't know what you've been in contact with.

7:00 Arrive home and wash hands well with soap and water. Make dinner, assume I'm safe. Wash hands and dishes, partner will appreciate (at least the dishes part) and I'll feel good about a full day, complete with active knowledge of where my hands have been.

9:00 get ready for bed, wash hands anyway, because as confident as you are, you're probably off by a bunch.

#Flattenthecurve

Eukaryotic Microbiology: The Blogs Are Coming

Despite my desire to keep updating the blog with course information, which has been an abject failure in regards to updates, I still want to post when I can. To be fair, I'm behind on grading, so I can't in good conscience be blogging about the course when assignments need to be graded.

However, I'll take a minute to make this brief post. It's getting to my favorite time of year: Student Blog Posts at Traveling Small with a Nucleus! I know for many students this is a writing assignment they truly enjoy. (Of course I'm sure some students do not like this assignment, but I have yet to hear from them.)

S0, I invite you to check out some previous students posts in the interim. The majority are quite good and there are some real gems in there. It's possible TSw/aN may be invaded with some organisms lacking a nucleus too. I'll keep you posted. 

Eukaryotic Micro: Week 3 the last of the fungi

So this week (actually last week) we covered what is probably the last unit concerning fungi: Cryptococcus neoformans. The first two weeks covered two ascomycetes, Candida albicans and Fusaruim species, and now we move over to the basidiomycetes, otherwise known as 'if I asked you to draw a fungus this is what you would draw'.

The primary research papers were:

• Polyploid titan cells produce haploid and aneuploid progeny to promote stress adaptation. Gerstein AC, Fu MS, Mukaremera L, Li Z, Ormerod KL, Fraser JA, Berman J, NielsenK. MBio. 2015 Oct 13;6(5):e01340-15. doi: 10.1128/mBio.01340-15.
• Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. Huang M, Hebert AS, Coon JJ, Hull CM. PLoS Genet. 2015 Aug 27;11(8):e1005490. doi: 10.1371/journal.pgen.1005490. eCollection 2015 Aug.

This is an interesting point in the semester. Upon completion of this week, we are ~25% of the way through the semester and exactly 25% of the way through the 12 modules. This is the point where students have completed the short writing assignment four times now, so hopefully they are comfortable with what I am looking for. I lay out the guidelines on day 1, and then model what I expect. There are two difficulties. 1: Getting students to explain a dataset of their choosing such that someone would walk away knowing what was done, what it showed, and most importantly be able to ask informed questions about the data set. Students are reasonably good at explaining the data after a week or two, but struggle to give enough experimental information such that you would know how the data was obtained. 2: Identifying limitations with the data set. This is in fact difficult, but it is an important skill to foster if we really want people who are critical thinkers. I ask them that their limitation answers the question 'how does this affect the authors' conclusions or interpretations?' This latter issue usually takes a couple more weeks to get better at for most of the class.

Cryptococcus neoformans normal and titan cells

It's also interesting because Cryptococcus follows up the ascomycetes we already discussed extremely well. Like Candida albicans, C. neoformans is a budding yeast, which is distinct from Fusarium, which although more closely related to C. albicans, is a filamentous fungus. However, like Fusarium, C. neoformans forms dikaryotic filaments during sexual reproduction and grows in a filamentous form during asexual spore production. 

I like these two papers (this is the first year I've used the Gerstein paper) because they deal with different aspects of development/differentiation in different ways.  The Gerstein paper is focused on a role titan cells play using primarily genomic approaches; the Huang paper is focused on spore formation and development using classical genetic approaches.

Gerstein et al ties in conceptually with the Selmecki and Ma papers from the Candida and fusarium modules respectively. All are centered on the acquisition of additional genetic information and the outcomes of this. I'm certain creationists always talk about the inability for an organism to acquire new 'information'. Well here are three independent examples.

Huang et al ties in, slightly, with the Lui paper from the Fusarium module by dealing with cellular differentiation and development. This is something we will come back to in the future frequently and is a biological concept I think is often underappreciated in microbes.  

First Eukaryotic Microbiology Classes

Since we do not start classes until after Labor Day, the first week represents a Wednesday, Friday week for my writing intensive Eukaryotic Microbiology course. I designed the course to run on a M/W/F cycle, so this first W/F week might seem problematic, but it is not. In fact, it works out extremely well.

The first day of class (today), involves discussing what is going on in the course and going over the syllabus. Similar to last year, in the first class I try getting students involved by having describe their goals and defining plagiarism. This year I focused the first lecture on the structure of the course and less time going in detail on the syllabus. It was only partially successful because I didn't get through the course set up but got through most of it. Luckily there's time to finish on Friday.

Although I don't get too deep into the syllabus (the students can read), I do cover grades and how they are determined because this is an issue that cuts to the heart of many students. One thing I started doing last year in another class, is determining the course GPA. That is the GPA for the course, determined by the student grades. The last two years my Eukaryotic Microbiology course had a GPA of 3.0 and 2.7. I'm pretty happy with these GPAs overall, it means I am not giving out a ton of A's but the GPA is higher than one might expect for an introductory class (this is not an introductory class and is taken primarily by seniors in the major with a smattering of graduate students).

The class is generally set up as follows:

• Monday: I give a standard lecture introducing the students to an organism and the relevant topics for the week.

• Wednesday: Students present primary research papers. However, they don't actually present the paper, I have them answer some specific questions:

• A. What question is the paper addressing and why do we care?
• B. Which conclusion do you think is the most interesting/important and why?
• C. Pick one figure that you think best supports your favorite conclusion and explain in detail how the data support the conclusion.
• D. What are the limitations of the data?
• E. Why are the conclusions important?

Questions A and E are only answered by the presenters, which is why they are struck out. These questions are derived from a document by Little and Parker (no longer available online, but they were at the University of Arizona). I like these because they focus the students in on a specific aspect of the paper, their favorite conclusion, which may be completely different than the press release or authors' overall conclusion.

The students then focus in on the data that supports that conclusions and not the entirety of the paper. Essentially, I do not want the presenters to reiterate the paper to the class, everyone is required to read the papers so there is no need to reiterate them.

The most difficult part is finding limitations or some issue(s) with the data/interpretation of data. I think students are trained to accept the literature and not rigorously go after the authors and their arguments, which, is in a nutshell, how science works. This one takes time and experience to get good at. Even excellent papers can have issues and I think one of my jobs is to get students comfortable with finding issues.

One thing I haven't told the students about is that the presenters have to give a 30 second elevator talk about the paper. I started doing this several years ago and I think it is extremely important. Basically, if you were an author and someone in the grocery store asked you about your work, how do you explain cogently and succinctly such that they are impressed and glad their tax dollars are supporting the work.

• Friday: Discussion of things. This varies markedly and is dependent on the students. I have a discussion board for them to ask questions, raise issues, provide feedback, etc. I do not post to these boards unless things are going off the rails and try to keep it a student oriented discussion board. (Once a prof posts a comment, all additional comments cease in my experience.)

On Friday, the second day of class, I will model what I expect out of the student presentations. We are reading "Complementary Adhesin Function in C. albicans Biofilm Formation' by Nobile et al. I also provided a review article 'Adhesion in Candida spp.' by Paula Sundstrom.

I will give a 30" elevator talk and then give an oral presentation that covers answers to the above questions A-E. Students are required to provide written responses to questions B-D to get us started.

Starting Monday we really kick into gear, although we will stay with Candida albicans. FYI the topics we are covering are drug resistance and host environmental adaptation.

My goal is to keep blogging about the course throughout the semester.

Preparing for Eukaryotic Microbiology Class

For the second year in a row, my advanced microbiology course, Eukaryotic Microbiology, is up and running. Technically this is the 11th iteration of the course, but the second year I'm going to try and blog about the course concomitantly. So the website is went live to students today and has a bunch of business related things about the course and a the first few weeks of modules available.

Before we met, in just under two weeks, there is an online quiz and a number of introductory papers for the course as a primer for the students. The papers are:

• The eukaryotic tree of life from a global phylogenomic perspective. Burki F. Cold Spring Harb Perspect Biol. 2014 May 1;6(5):a016147
• The origin and early evolution of eukaryotes in the light of phylogenomics.  Koonin EV. Genome Biol. 2010;11(5):209.
• The hybrid nature of the Eukaryota and a consilient view of life on Earth. McInerney JO, O'Connell MJ, Pisani D. Nat Rev Microbiol. 2014 Jun;12(6):449-55.
• An archaeal origin of eukaryotes supports only two primary domains of life. Williams TA, Foster PG, Cox CJ, Embley TM. Nature. 2013 Dec 12;504(7479):231-6.
• The common ancestor of archaea and eukarya was not an archaeon. Forterre P. Archaea. 2013;2013:372396. doi: 10.1155/2013/372396.
• A new view of the tree of life. Hug LA., Baker BJ., et al. Nature Microbiology. 2016 Apr 11; 1(article number 16408)
• Predation and eukaryote cell origins: a coevolutionary perspective. Cavalier-Smith T. Int J Biochem Cell Biol. 2009 Feb;41(2):307-22.

Figure 1 from the Hug paper

I ask the students to read the Burki paper first, which is a great overview of the current eukaryotic tree and how it was established. The Koonin and McInerney next, followed by the Williams and Forterre papers. There's a fair bit of overlap among the Koonin, McInerney, and Williams papers that I suggest they skim through. Once those are done, I ask that they read through the Hug paper, which is the only primary research paper of the list. Finally,  the Cavalier-Smith paper on what is a eukaryotic cell in some detail.

I particularly like the two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not. 

Student Editorial and Missing the Point of College

Today represents an awakening for me. I was browsing the student newspaper and came across the following editorial: 'Professors owe us study guides'. My first thought was 'what the hell!', but I quickly remembered that titles are generally not written by the authors. So I decided to read the thing, I suggest you do the same. I'll wait. Sorry if you're now thinking Trump is a good choice, not my fault it was the editorial writer's.

The author starts out reasonably enough "With midterms in full swing, many of us at the University of Minnesota have been studying diligently to prepare for our exams. As these assessments often represent a large percentage of our grades, it’s very important to do well on them." It's good to hear that you are studying diligently, seems appropriate being that you're an adult in college and all. But there's already a whiff of something problematic, the focus on the grade. Yes grades are important and you should want to do well on your work in order to obtain good grades. However, grades in and of themselves are a means to an end, they are not the end.

The problem is manifest in the third and fourth sentences, which encompass the entire second paragraph. "But there’s nothing more frustrating than trying to study every little tidbit of information you’ve learned since the start of the semester. It simply isn’t going to happen, especially because students often have more than one midterm exam." There is so much fail embodied in this, I can't even. First, if you are studying every little tidbit of information, then you probably never spent any time during your education to think about teachers and professors and tests, quizzes, exams to realize that people have personalities and to use this information to strategically study. Is something emphasized over and over (probably a good idea to study it), was something highlighted as important, meaningful, or a key point (probably a good idea to study it). Was something mentioned once as a brief aside, maybe in response to a question (probably not worth spending much if any time studying). As this is spring, almost certainly this semester represents at least the second semester the editorial writer has been at the University of Minnesota (there's a small possibility they just transferred in). Second, we actually know that students have mid-terms around the same time. It's weird, because at the end of a semester there's this thing called 'finals week,' where all the professors schedule exams over a few days, but none of us know the others do the same thing. Third, I hate to tell you this but it does happen. Maybe not with you, but many students do learn a lot of material. I know I've given out the A's to prove it. I've written letters of recommendation for students with 3.85 GPAs. Just because you cannot be bothered or feel like it's too much of a burden, well WAH. But here this is just for you:

Fourth, you need to realize that it is a University of Minnesota policy that on average a student should expect to spend three hours a week per credit of class. So a three credit class means ~ 9 hours of week of in class and out of class work. Maybe some weeks you work 5 hours, exam shows up and you work 10 hours, your average is still less than 9 hours a week. And to be clear that three hour average/credit is for the average student to receive an average grade aka a C. You want a better grade, you should expect to work more hours on average. (Now might be a good time to wash your hair again.)

For full disclosure, I know many classes expect much less work than this. But these classes are in fact screwing you over. My primary class, which I uniformly have received excellent student evaluations for. students note how much work the class is and ask that the credit load be increased because it's so much work. However, most students that note the work also fill in the 6 - 9 hours/week  on the scantron (for my 3 credit class). Realize that a full credit load of 15 credits, represents slightly more than a full-time job commitment (45 hours)!

Ok that deals with the generic dome-a-dozen complaint about studying (you're not in high school anymore). This really isn't more than what is complained about every single year. My problem is with what comes afterwards "Study guides help students to focus their efforts and weed out concepts that won’t be on the exam. This can save a huge amount of time. Not to mention, by ignoring the concepts that won’t be tested, we can spend more time on those we’re expected to know, increasing our understanding of the material and, hopefully, our test scores."

The arrogance of those twisted sentences represents much that is wrong with the approach students have towards a college education. Some, like this letter writer, consider college an extension of high school. It's something they have to do and is mostly a waste of time. I thought much of high school was a waste of time, but that was because I didn't know any better. The difference is that I was required to get an education through the 12th grade, or at least it was a serious issue to drop-out and not something that could be simply accomplished. Not so, with college. There's no law requiring post-K-12 education. I realize to get many jobs a college education is required even if in reality it isn't. But you know what, many jobs, including good jobs, do not require a four year degree.

Let me explain something to our entitled editorial writer and those who agree with them. What we teach in class is important or at least it is considered important by an expert or experts in the field. Courses have to be approved by a committee based on what the learning objectives are and how they will be presented and how they will be assessed. To adequately test someone on their grasp of the material, it usually means your are asking focused questions on specific areas. Because something isn't on the test does NOT mean it is not important to know or needed for subsequent classes. You are not in college to take the fucking tests and I apologize that the ACT/SAT companies, politicians, and standardized testing has you thinking it is. You are correct, if we tell you what to study so you can vomit it back to us, you will get better grades more easily. That isn't the fucking point. Also, how can you suggest that if you spend more time studying fewer things, you will increase your understanding of the material. No, you will not, you will only know a part of the material well and even then probably only well enough to recognize words on a multiple choice exam.

"Not all professors allow students the luxury of having study guides, however. As someone who cares tremendously about my grades, there’s nothing more frustrating than having to study extra information that’s not part of an assessment. The less information I have to worry about knowing, the better I’ll learn it and be able to recall it in the future." See you should not be at a university. I'm sure you're smart, at least from a standardized testing every child in the community regardless of proficiency goes high school standpoint. But you are missing the point (that sound you just heard, that was the point flying by). The point of college is not your grade. Sorry, it's true, time to grow up. You care tremendously about your grade, no mention of knowledge or understanding. Simply your grade. Truly the writer makes me weep and gnash my teeth simultaneously.

I especially love this thought: the less I have to learn, the better I'll be able to learn it. Well no shit Sherlock, no fucking shit. It's kind of like asking for a raise and justifying it by saying I can buy more stuff. Also, if recall is your goal, you're doing it wrong. Life is not, I repeat (because it might be on the exam) not a fucking multiple choice test.

Finally we end with, "For these reasons, I think it’s incredibly important for the University to require professors to provide students with comprehensive study guides. Each individual college could delegate specific guidelines, but the policy should encompass the entire University." Well letter writer let me end with a comprehensive guideline for my upcoming exam: T, F, T, T, B, C, C, A, E, D, D, and more than 14.

Eukaryotic Microbiology Intro Readings

My advanced microbiology course, Eukaryotic Microbiology, is up and running. At least the website is. I have assigned several introductory papers for the course as a primer for the students. The papers include:

• Predation and eukaryote cell origins: a coevolutionary perspective. Cavalier-Smith T. Int J Biochem Cell Biol. 2009 Feb;41(2):307-22.
• The origin and early evolution of eukaryotes in the light of phylogenomics.  Koonin EV. Genome Biol. 2010;11(5):209.
• The hybrid nature of the Eukaryota and a consilient view of life on Earth. McInerney JO, O'Connell MJ, Pisani D. Nat Rev Microbiol. 2014 Jun;12(6):449-55.
• An archaeal origin of eukaryotes supports only two primary domains of life. Williams TA, Foster PG, Cox CJ, Embley TM. Nature. 2013 Dec 12;504(7479):231-6.
• The common ancestor of archaea and eukarya was not an archaeon. Forterre P. Archaea. 2013;2013:372396. doi: 10.1155/2013/372396.

From McInerney et al

I've used the Cavalier-Smith and Koonin papers in the past to introduce the basic ideas surrounding where eukaryotic cells come from (I think the Koonin paper is more clear here) and what is a eukaryotic cell (Cavalier-Smith wins here).

This year I've introduced the other three papers to provide additional perspective on the origin issues. The McInerney paper does a good job summarizing the four basic hypotheses for the origin of the eukaryotic cell (see the figure) and I think it is good to come after the first two papers as they deal more directly with the science behind the origin of eukaryotic cells.

I particularly like the last two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not. 

First Class in the Books

The state fair is over indicating the end of summer and the beginning of a new semester. I taught my first class today, which of course means I basically met the students and introduced them to the course. In other words, we went over the syllabus…kind of. The course I am talking about is Eukaryotic Microbiology, an upper division course that focuses/uses the primary literature to teach students about eukaryotic microbes, scientific thinking, argument, etc.

The third slide in this lecture is the following (from here with slight modification)

This slide gets used throughout the course but I use it in the Introduction lecture to highlight how little almost all students are familiarized with the diversity in the eukarya. Basically students are familiar with green plants at 12:05, fungi (except for the microsporidia) at 3:15, and the animals, including sponges, at 4:00. Other than the Opisthokonts (in blue) and a minor fraction of Archeaoplastids (in green), the vast vast diversity of the eukaryotic lineages are basically ignored in biology courses. Admittedly there is lip service played to Plasmodium falciparum (the primary agent of malaria) over in the Alveolates. But just look at how little is brought up! Of the eight major eukaryotic lineages, only two are routinely discussed, think of all the biology out there we know so little about! This, in my opinion, is incredibly exciting.

Aspects of this problem were recently brought up by Larry Moran and PZ Myers (by way of   Jeffrey Ross-Ibarra). Again all that diversity noted above falls into the choice C.

Now that I hopefully have instilled some small sense of awe or at least lighted a candle of interest in my students, we deal with the syllabus and some course specific issues. I do want to point out this course is writing intensive, which means a bunch of things but basically we do a fair amount of writing (surprising huh?).

There are two things we did today I want to mention. First, I asked them what their goals are in relation to the course. (Other than getting an A.) So I had them spend a couple of minutes writing down their thoughts and then we discussed them. This represents one easy way to get the students talking in a relatively stress free environment. Open discussions are an integral part of the course and the sooner I get students comfortable speaking up the better. My goals were: 1, to give the students a broad sense of that importance of eukaryotic microbiology; 2, to increase their fluency with the scientific literature; 3, to hone their critical thinking skills. I won't divulge the students' goals.

Second, we discussed plagiarism as it is a writing intensive course. I have found that students know what plagiarism is, but if you ask 20 students for a definition, you'll get 12 - 15 different variants. I also have the students write down what they think the consequence for plagiarism should be. This leads to yet another relatively stress free discussion and serves develop a sense of student ownership for the course. Once the discussion is complete, we agree to a definition and consequences that is posted onto the course website. This year we came up with:

The 4161W class of 2014 has agreed to define plagiarism as not giving credit for others' work, including words and ideas, that is not common knowledge.

and the penalty:

Students who are found to have plagiarized will receive an F on the assignment and be reported to the Office for Student Conduct and Academic Integrity for the 1st offense. A subsequent offense will result in an F for the course and another report to the Office for Student Conduct and Academic Integrity.

As normal for the first lecture, I did not get through everything. Luckily Friday allows time to finish up going over the course and to discuss our first paper. This discussion allows me to demonstrate what I expect of the students when they do presentations and gets the students started reading papers. The paper we discuss on Friday is:

Complementary adhesin function in C. albicans biofilm formation. Nobile CJ, Schneider HA, Nett JE, Sheppard DC, Filler SG, Andes DR, Mitchell AP.Curr Biol. 2008 Jul 22;18(14):1017-24. doi: 10.1016/j.cub.2008.06.034.

Response to poorly argued opinion on student evaluations

This week the campus paper published an opinion piece by Harlan Hansen, professor emeritus, College of Education and Human Development entitled 'The missing factor of course evaluation discussion' with the subtitle 'The University should use its best faculty to teach and improve others.' I have commented previously on the issue of student evaluations and release of information to prospective students. Despite a previous attempt to have student evaluations released, which failed by a large margin, the proposal will not go away. Basically, I think the administration and associated faculty who want the information released should simply mandate that the information be released and send a big 'and fuck you too' to the 90% of faculty who do not want student evaluation information released. Otherwise, it seems like we will just keep discussing and voting on it until the vote comes out the right way.

Regardless, I want to rant about this opinion piece for several reasons.

First: the first paragraph or as I like to call it, holywhatthefuck!

When I arrived as a faculty member of the University of Minnesota in 1968 I remember a publication that rated course instructors. A few years later, I believe, it suddenly ceased publication because of faculty requests, I assume. Forty-three years later, the request for that information by students is still a nagging question.

Can you find all the logical fallacies? So in 1968 there was a publication that ranked course instructors. I will accept this position at face value, but I have some questions: was this information disseminated to the student body and if so how? Was this information disseminated to the faculty as a whole and if so how? Was this information used by students to help decide which classes to take? How were course instructors rated? Did this information rate every course and every instructor, including non-faculty instructors (I'm assuming some courses/labs were taught by graduate students in 1968, though this may not be the case.)? I'm not sure if Dr. Hansen realizes this or not, but technology and dissemination of information is fundamentally different in 2014 than it was in 1968.

Then we get to the second sentence, which includes both 'I believe' and 'I assume'. I cannot help but wonder what kind of academician Dr. Hansen was. Let's accept that this publication existed and ceased publication in the early 70s. Why should we assume that it ceased suddenly (did you hear the ominous music just then?) because of faculty requests? Dr. Hansen simply assumes it. Here are several other possibilities: maybe no one went to the library to obtain this voluminous publication to help choose courses or for any other reason, maybe it was out-of-date by the time this information was published (remember this was before computers were collating all the information via scantron forms and then imported into excel spreadsheets for rapid organization), maybe the costs associated with the publication were not off-set by the usefulness of the publication. See there are three other possible reasons without even trying. Your assumption carries no weight.

Finally, we get to the last sentence, which has little to no linkage to the previous sentences. Have students been requesting this information for 43 years? Is it really still a nagging question? In 1983 there was an outcry for instructor rating information, even though that information wasn't actually collected and therefore didn't exist? A student who turned in  a paragraph like that in my classes would not fare well. But alright, let's assume an editor took out all the cohesion in the introductory paragraph setting up the issue to be addressed.

Second: unsubstantiated claims or as I like to call it, pullingshitoutofmyass, I assume.

Consider the following points made by Dr. Hansen:

"students say they want information that will lead them to more interesting and effective professors. Second, faculty who were quoted in the news minimized the students’ requests as wanting easy courses with high grades by instructors who tell good jokes."

I'm sorry but isn't an instructor who tells good jokes generally considered more interesting? Regardless, I have to concur that many, not all, students would rather have an easier course on a topic than a more difficult course on that topic. I could be wrong, but a slightly earlier opinion piece published in the campus paper seems to support my position.

"relative to my years of experience at the University, ratings of faculty instruction do not change over the years." 

I would not be surprised about this, but data please. Also, how the hell does he know? Didn't this bible of instructor ratings stop being published in the early 70s? Maybe he was department head and saw the student evaluations (when we actually had them), which would raise the question, why didn't he provide training for his ineffective faculty?

"“A” and “B” instructors have no problem sharing their ratings" 

Again data please. Hell, I'll even provide a data point, on my student evaluations using a 6 point scale (6 being being the top score), I fall well above 5 in almost every category every year. In those remaining categories I still fall above 5 every year. So, does this make me an 'A' or 'B' instructor? It seems like it should, and if so count me as an instructor who has a problem sharing my ratings.

Third: problem solving. 

By establishing the problem using holywhathtefuck and pullingshitoutofmyass approaches, Dr. Hansen then proceeds to assign blame. See it's not just the ineffective instructors, it's an administration problem. (Again I want to stress we have never defined effectiveness or established criteria to quantify effectiveness other than student evaluations, which are best correlated with students' expected grade.) And now we get to the solution:

"The president of the University should charge deans and department heads to put in place programs that can help all instructors improve over time."

Personally, I think these programs are useful and important. However, I wonder where the resources are going to come from for deans and department heads to do this. Programs do not come from the vault of readily available no expense resources. This solution also raises the question, why don't faculty development programs exist already? The answer is that they do, I have attended several. I wonder when Dr. Hansen retired such that he is unaware of them. Admittedly, these programs are voluntary, but they do exist.

Of course Dr. Hansen does have a remedy to this apparent lack of teaching development:

"The key factor is assigning current colleagues who have demonstrated quality teaching skills to share and demonstrate with those in need. While this may appear threatening to individuals, it establishes a community of scholars within each unit where, eventually, everyone can share positive techniques with each other."

Yes. because nothing rewards successful teaching like getting more work and responsibilities to train and manage the ineffective instructors. Don't forget, these are the same ineffective instructors who really don't want to get better as Dr. Hansen noted above when he states that faculty instruction does not change over time.

My opinion of the opinion: from here.

I am still surprised by the whole student evaluation movement. We have no good data suggesting that student evaluations gauge effective instruction, some studies do suggest this but many others do not. I have heard from colleagues that students simply want more information about a course and god forbid they go to some commercial site like rate my professor. Well I am all in favor for more information as long as that information is valid for what you are attempting to learn/show. Student evaluations do not, I repeat not, seem to correlate with effective or quality teaching, so what information are the students receiving about a specific course/instructor? The student evaluation is being changed to ask the following questions, which are relatively minor changes in wording compared to the current evaluation:

1. The instructor was well prepared for class.
2. The instructor presented the subject matter clearly.
3. The instructor provided feedback intended to improve my course performance.
4. The instructor treated me with respect.
5. I would recommend this instructor to other students.
6. I have a deeper understanding of the subject matter as a result of this course.
7. My interest in the subject matter was stimulated by this course.
8. Instructional technology employed in this course was effective.
9. The grading standards for this course were clear.
10. I would recommend this course to other students.
11. Approximately how many hours per week do you spend working on homework, readings, and projects for this course?
   • 0-2 hours per week
   • 3-5 hours per week
   • 6-9 hours per week
   • 10-14 hours per week
   • 15 or more hours per week

Of these questions, only those in blue are proposed for release to the students. Questions 7 and 10 seems to provide useful information on whether the student liked the course or not.  Question 8 is irrelevant to the discussion of instructor rating for the most part. Questions 6 and 9 may provide insight into the instructor's effectiveness and fairness. Question 11 is the great equalizer. If two sections of the same class are different here, which do you think a student would gravitate towards? This is not minimizing student concerns, I would rather take a course that required less work too other things being equal. 

You may be asking, 'Why the hell aren't questions 2, 3, and 5 being released?' Good question, as these seem key regarding a student's ability to decide which courses they want to take. Courses do not exist in a vacuum, without an instructor we might as well attend google university and write papers on vaccines and autism. Those questions are not being released because they may reflect specifically on an instructor. (Duh!)

Of course we must consider what ever will a student do without online released student evaluations? I mean what has happened over the last 43 years! If only there were some way one student could relate information to another student about a course. Some form of communication, I don't know, like texting, or tweeting, or posting to any number of social media sites, fuck maybe they could simple open their mouths and have words come out in the direction of another student's ear. If only. Sadly, I doubt our students are even aware of these modes of communication.

Poor US Education Meme Infects the Minnesota Daily

It's bad enough reading the standard misinformation regarding K-12 education in the popular press, but now it has infected our student paper too. The editorial compares the curricula of Germany with that of South Korea as educational systems that could be modeled to improve US education. But the question, the answer to which is assumed in this editorial, is, is the US education system doing poorly?

Dunces unite

Based on the popular press, you'd think US education is in complete disarray. This idea is supported by tests that compare the US to many other countries.

For example, Pearson ranks the US as 17th overall in cognitive skills and educational attainment (Finland, South Korea, Hong Kong, Japan, and Singapore rank 1-5). The US is between Belgium and Hungary and for the record Germany comes in at a devastating 15th. These rankings spanned 2006 - 2010.

Furthermore, the Programme for International Student Assessment (PISA) 2012 rankings have US 15 year olds at 17th in reading, 23rd in math, and 21st in science out of the 34 Organisation for Economic Co-operation and Development (OECD) countries. (The US ranked 36th in math of all countries/areas tested.) 

Highlander ranks higher than
US in math and kicking ass

These rankings are problematic for several reasons.

Zero Sum Games: For the US to move up in its rankings other countries must go down. As the Highlander says 'There can be only one.' Is the US education system likely to be that much stronger than education system of the United Kingdom? Germany? Japan? Canada? France? Belgium? I'm not suggesting we should not try to attain the greatest achievement possible, but don't you think these other countries want to have student success? Even if we thought of it first (we didn't), other countries would likely have noticed and followed suit.

Apples and Oranges: The US is not a monolith of education. If anything we're a monolith of stupidity. We have a decentralized education system. Each state can do what it wants, thus states like Tennessee and Louisiana, which overtly teach biblical creationism, may do poorly on science exams. Using the US as a single entity for comparison sake does reveal major shortcomings in our educational system. But it's basically worthless, unless your goal is to eliminate public education and replace it with a mechanism to move more taxpayer money into corporate hands.

From Slate

 If we look at states individually, something different emerges.

On the PISA exam, the US math average was 481, placing us at 36th of OECD. The average for the OECD countries was 494, putting the US well below average. But if we look at individual states we find that average in Massachusetts was 514, Connecticut was 506, and Florida was 467. Two states doing well above the OECD average and one state 4 points below Croatia, a country recently established from the ruins of Yugoslavia.

Similar results are seen in the science averages. US average: 497; OECD average 501; Massachusetts average 527; Connecticut average 521, and Florida average 485.

Any guesses on reading literacy? US average: 498; OECD average 496; Massachusetts average 527; Connecticut average 521, and Florida average 492.

Do you see a trend there? It looks like some states, Massachusetts, do extremely well helping promote a strong US score. Yet other states, I'm looking at you Florida, fuck it up for everyone. You'ld think the talking heads would be asking 'what's working in top performing states like MA, NH, MN, etc?' or even 'what's not working in bottom performing states like FL, MS, AL, etc?'

I bet people in Massachusetts really want to overhaul their successful education system in order to try out a new one that might improve Florida's scores.

We spend so much time disparaging teachers that many rankings done in the US use teacher tenure, teacher seniority, and charter school availability as major criteria in their evaluations of state education. Regardless of student outcomes! If a state has teacher tenure and great student achievement, should that state be dinged? For example, the American Legislative Exchange Council (not affiliated with Congress) came out with their rankings: Massachusetts received a C; Florida a B.

I suggest you go back on look at the PISA scores and then let that digest a minute. If you think the PISA test is a Muslim plot, you could also look at the USA USA USA National Assessment of Educational Progress NAEP rankings: MA, with MN and NH, first in 4th grade math; Fl 30th. MA first in 8th grade math; FL 37th. MA, first in 4th grade reading; FL 13th. MA first in 8th grade reading; FL 33rd. (Was that a complete sweep?) Yet the ALEC says FL is a clear letter grade better than MA. WTF?!?! (ALEC cares little about education and more about policy that ends public education: Vermont and Rhode Island received D+'s yet were 2nd and 6th in the country on the NAEP tests respectively; Utah B- and South Carolina C were 41st and 50th on the NAEP test respectively.)

For the record, MA and other top performing states do well across economic spectra. These results are not simply due to socio-economic differences. However, poverty clearly has a profound effect on education achievement. 

Coming full circle, it's not a zero sum game here either. For FL to improve its ranking other states have to lose positions. The point is that using the US as an education collective to compare against actual education collectives is ridiculous.

Regardless, I am tired of hearing about the travesty of the US education system, when in fact many states are doing great, but are dragged down in national surveys by poor performing states (I'm looking at you deep south). We should look at the data coming from these assessments and tests and determine what is valid (are students in Singapore better prepared for the test due to timing of the curricula? do all students go to school and are they all tested in China?). We should also celebrate our accomplishments, YAY Massachusetts, and recognize our problems, I'm looking at you Florida, I'm also looking at Minnesota which is doing great on these tests but still has a huge achievement gap.

So thanks Minnesota Daily for getting me to write this. For the record, we don't need to look to South Korea or even Germany to fix our education system. First, we have to realize the US education system does not exist, so it can not be broken and need to be fixed. Second, we only have to look at our neighboring states to see what works and what doesn't. Third, if there are applicable educational innovations developed overseas or even up North, I'm all in favor of trying them. But realize much of our system works well and let's not fuck it all up because of Florida.

My Favorite Time of the Year

From here

One of the courses I teach culminates with blog posts written by the students. This is the third year I have used this assignment and is one assignment the students actually enjoy doing (at least based on student feedback from previous years). Students will be submitting their final essays on some aspect of research on eukaryotic microbes in the next few days and you will be able to find them here. Until the new ones are posted, you can see some essays written previously.

FYI: The assignment is to write an essay of 1000 - 1500 words for a lay audience of science enthusiasts that incorporates at least primary research papers on a eukaryotic microbe. (Microbe being defined in the course as an organism that exists primarily as a single celled organism, thus excluding microscopic multicellular animals.) Students were allowed to write in any voice and use any style of writing.

If you read through an essay, please leave a comment for the student.

Teaching Critical Thinking

One question I grapple with is 'how do we get students to ask questions about, or rather to question, peer reviewed research papers?' This is based on my experience that undergraduate students and even many introductory graduate students have difficulty grasping the concept that there may be issues or even important problems with peer reviewed research. Part of this is based on an inherent appeal to authority/self confidence issue, how could a lowly undergraduate find something problematic with a paper written by Ph.D., or equivalently trained, scientists.

Why We Care About Critical Thinking

However, the question I am grappling with is just a subset of the more important issue, how do we teach students how to ask the 'right' questions. The key here being 'right.' This is a fundamental aspect of critical thinking. Being able to identify the assumptions, biases, controls needed, discrepancies, etc. in an argument, and a peer reviewed research paper is nothing if not an argument. I find the most successful approach is to identify these, and other, points by asking questions. Again these question have to be the 'right' questions.

In my advanced undergraduate class, I can usually classify my students into 3 categories: the non-questioners, the trivial questioners, and the rare critical thinking questioner. By the end of my course, I want my students to find themselves generally in this latter category.

In the first category, the non-questioner, we find the shy students who are uncomfortable speaking up. This silence could be the result of inherent shyness, poor classroom experiences, or even cultural issues. In fact, this point of 'cultural issues' reminds me that it is important for me to remember that women and minorities are frequently ignored or blatantly omitted from discussions. In my experience, there are as many if not more women promoting the discussions in my course as men. Regardless, I try to address the issue of cultural differences early by calling on women and minorities during our 

The Shy Student

discussion sessions. Included in this category of students are those who are not confident with the material and thus do not want to speak up for fear of saying something stupid. I provide many resources and tools to help bring students up to speed if they are missing some background, so I tend to be less sympathetic with these students because they, by definition, must be aware of their deficiencies and choose not to address them. Of course, it takes awhile to separate these students from those who are shy, but it is disheartening to identify a student as being  intellectually lazy, lazy in general, or indifferent. To be clear, I have had students that lack some of the foundational material needed for my course that have worked hard to address these issues, and I help them as much as possible, having one on one meetings as much as they need to go over concepts, specific papers, etc. I love these students, because they have a drive that is infectious. Getting back to the shy students, how can I help get them engage in the course, such that they can move to category 3 and without having to change their personalities? For these students, all students actually, I have online components to the course. In addition to in class discussions, I have an online forum to initiate new discussions or continue discussions started in the classroom. This provides a place for those students who are inherently shy and students who are not comfortable thinking on their feet, which is what the classroom discussions entail. Students can use these forums to ask broad questions, initiating discussions beyond the minutiae of the papers they read. Students can also ask for help if there is something in the papers, a method, conclusion, etc. they do not understand, and students can help their colleagues by answering those requests for help. While I monitor the discussion boards, I refrain from commenting as much as possible, such that it quickly becomes a student-driven environment. While not perfect, there are mechanisms to promote moving students from category 1 to category 3.

Were you there? Only applies
to science not the New Testament.

The second category: the trivial questioner, is the place I work the most. Not that a specific student is a constant trivial questioner, but rather it is a constant place we come back to in class. This is not a problem because it does serve as a constant 'teachable moment.' The trivial questioner falls into the meme that there are no stupid questions. Of course there are stupid questions! In fact, the 'there are no stupid questions' comment is itself a stupid comment. I understand the 'there are no stupid questions' concept, but it is used with the tacit understanding that everyone is acting in good faith. This is seldom the case. For example we have Ken Hamm's 'Were you there?' question. This question is bullshit and not acting in good faith. The fact he encourages ten year olds to ask this question just serves to exemplify the moral vacuum in which Hamm resides. Hamm knows this question is a bullshit question, but it is a nice soundbite gotcha-sounding question to the masses. However, the ten year olds Hamm sends out to 'ask' questions do not know why this is bullshit, and that is his goal. However, we can use it as a teachable moment. The problem, in my opinion, is that Hamm knows many children would never ask the question, but will think the question and then answer it for themselves. In my course, there are many 'were you there?' type questions. Not necessarily from the Hamm perspective, but from the 10 year old perspective of 'this sounds good, I'll go with it' perspective.' These kind of questions are particularly present at the beginning of the course and I like to think I help move the students into the 3rd category. It's possible that I push these students into the 1st category, but I doubt that based on the quality of the discussions as the semester progresses. By way of example, every year when discussing a paper using a mouse model, the question will arise 'well I am concerned that the study only used female mice and I wonder what the data would be if male mice were used?'  This kind of question is relatively easy to come up with because we teach students 'black and white' thinking, everything is a binary decision. So when the student reads the methods and materials and sees '20 female C57/B6 mice were....' the student immediately thinks 'male' or vice versa in a 'tell me the word that pop into your head when I say...' kind of way.

So how do I encourage questions/comments of these 2nd category students without pushing them into the 1st category? What I have found works is to mimic Socrates, I ask questions. For example...

I am concerned that the study only used female mice and I wonder what the data would be if male mice were used?

Why do you think this might make a difference? I agree that there are important differences between females and males, I'm wondering how you think these differences apply to this study?

Well there could be differences due to hormones or something...

That's a great point, because that is clearly the case in certain instances like Paracoccidiodes infections. Is there anything in this system that makes you think there is would be a sex-based difference?

.....

Ok that's a good point at face value, but maybe needs further consideration, did anyone have additional issues with this study?

The point is to encourage/require the students to have a scientific justification for their concerns, questions, critiques. This, in my opinion, is the most difficult thing the students can learn and that I can teach. The point is that I need to teach the students how to question the studies, but also to question their own questions/concerns. But, I want to emphasize that it is ok to be wrong! We talk about well conducted studies that have generally solid conclusions and identify potential concerns. These concerns may not change the overall conclusions, but do raise concerns with sub-conclusions that may not be valid. In fact, the introductory paper we are discussing is the one I railed on previously. We will also be considering the press release. This is a change from the last couple of years when we discussed a well written, described, and assessed paper. I'm interested in how this approach works.

Own this book!!! 

Finally, we come to the third category: the critical thinker questioners. For these students, I can only refine their skills, improve their writing, and expose them to new and interesting areas. Almost uniformly, these students have research experience and likely significant experience. However, these students almost certainly have holes based on the areas they have been exposed to. These students know the potential issues in the area they are familiar with, but lack the similar approach/mindset in the areas they are not familiar with. This is one of the reasons it is essential for scientists to read well outside their fields. Breadth of knowledge promotes a better assessment for how your studies fit into the broader world of science. This increases the impact of your research not only from the study in question, but also in the questions you ask in the first place.

FYI. While I have categorized student comments/questions into 3 groups, no one student (nor the instructor) fits into a given group. Furthermore, I love my course because I learn so much from the students, even those that tend to cluster in a specific category. The lessons I learn may vary, but I learn important concepts, holes, insights from all three groups.  I thank the students from previous years for helping me develop these insights and to improve my courses.