Field of Science

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:
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. 

Donald Trump and Climate Change: California edition

So here's what the potential dumbass-in-chief had to say in regards to the lack of rain in California over the last few years: "there is no drought." And he follows up with "If I win, believe me, we’re going to start opening up the water, so that you can have your farmers survive so that your job market will get better,"

This is how I envisions Trump's understanding of how droughts work:

and how he'll fix it:

easy peasy

Best Rock Albums of the 80s

Over at Patheos, Ed Brayton as a child of the 80s posted his:

The Best Albums of the 1980s

As a child of the 80s myself, entering high school in 1983, and a music lover I thought I'd add my two cents (which was worth a lot more back then, although still not much more than two cents). Overall, I have a lot of overlap with Ed's choices of bands, although I often choose different albums. Also, I'm specifying 'Rock' albums, because there are other 80s albums I love that are not Rock. 

So, where we agree:

The Police – Synchronicity An amazing album Miss Gradenko, Synchronicity II, and King of Pain are some of my favorite songs. 
Peter Gabriel – So Got to see Gabriel in concert and he is amazing. 'So' fuses with The Police as Stewart Copeland plays some of the percussion on Red Rain. Regardless, 'In Your Eyes' is probably the best love song ever written. (and I'm not generally a fan of love songs.)
Guns n Roses – Appetite for Destruction Come on? Do I really need to comment? Mr. Brownstone, Welcome to the Jungle, It's so Easy....enough said.
Talking Heads – Stop Making Sense While I did not get the Talking Heads during high school, I discovered them during my early years of college. Kind of perfect for Stop Making Sense.
Eric Clapton — Journeyman (Ed also included August here, but although I was familiar with many of the tracks on the album, was not really in my wheelhouse.)
Where we agree on bands, but not albums:

U2 – Rattle and Hum (Ed picked the Joshua Tree, which I thought was overrated. I would have taken Boy or War, both excellent albums, over The Joshua Tree.)
Yes – Big Generator (Ed picked 90125, which is a great album. Big Generator resonated with me more and represented a memorable summer in my life. I could also put Robert Plant in here for 'Now and Zen' for that same summer.)
Where we part ways:
My Choices not on Ed's List
REM  — Fables of the Reconstruction (although Murmur and Document are in the running). How can you consider important music from the 80s and omit R.E.M., sure they're from Georgia, but they're from Athens which also has some great breweries.
Pink Floyd — The Final Cut and Momentary Lapse of Reason I know Pink Floyd is arguably a 60s or 70s band, but the Final Cut, which I actually discovered in the 90s, and Momentary Lapse of Reason are amazing albums for completely different reasons.

Def Leppard — Pyromania The 80s without Def Leppard is like the 30s without the Great Depression, why even talk about it?

Ed's Choices not on My List

Living Colour – Vivid (Great band and music that I am only recently coming to appreciate)

Public Enemy – It Takes a Nation of Millions to Hold Us Back Not my experience.

Prince – Purple Rain (Great artist but never quite clicked with me.)

Stevie Ray Vaughan — Couldn’t Stand the Weather (Excellent artist, but there are so many excellent artists....Santana...just saying)

Genesis – Three Sides Live (Look I love Genesis, especially before Peter Gabriel left, but they reinvented themselves extremely well with Phil Collins as the front man. I just don't have them higher on my list of definitive 80s bands. For a road trip 'Something in the Air Tonight' is a must.)

End point: If I redo this in 5 years how much overlap will there be? Will Duran Duran make the cut, Flock of Seagulls? Doubtful.

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.

What I Read (2015)

(Grade A-F, no E's) Title-Author Additional thoughts

B     The Bazaar of Bad Dreams by Stephen King. Some good, some less good, but mostly good collection of short stories.

D     Bleak House by Charles Dickens. Took me longer to read than it took Dickens to write I expect. Kind of got interesting ~80% of the way through, wrapped up a little too neatly.

    The Sandman Vol. 4: Season of Mists by Neil Gaiman. One of my favorite collection of stories so far in this series. What happens when Lucifer gives up control of Hell?

    Gotham Central Book 4: Corrigan by Greg Rucka, Ed Brubaker, Kano. Good analysis of a corrupt police officer and the effect it has on several other members of the squad.

B+    Gotham Central Book 3: On the Freak Beat by Greg Rucka, Ed Brubaker, et al. Good integration of the police dealing with supervillians and problems associated therein. Didn't like the introduction of a superpower to a police officer (psych ability), which defeats the purposes of stories.

    The Fifth Season by N.K. Jemisin. A new world with a new culture. Not sure where this series is going, but Jemisin sets up an intriguing world.

C+     Symbiont by Mira Grant. Not as good as the first part of this trilogy. Felt a lot like filler, main plot really didn't move much.

B-     Gotham Central Book 2: Jokers and Madmen by Ed Brubaker, Jim Starlin, Michael Lark. A good follow-up. What happens when a normal police have to deal with The Joker. Ultimately Batman saves (most of) the day, so it didn't work out as well as I would have liked.

B      Deathpunch'd by Jeremy Spencer. Humorous and scary, discussing drug addiction and life in a upcoming band. Got a bit repetitive though.

A-     Doctor Sleep by Stephen King. One of my favorite recent King books since I read 11/22/63 or It. The kid from The Shining all grown up.

B-     The Alienist by Caleb Carr. I realize this came first, but I liked The Angel of Darkness much more.

    A King's Ransom by Sharon Kay Penman. Historical fiction is interesting. Taking known events and people and trying to write the story of how things unfolded is an interesting genre.

    Informal Logic by Douglas Walton. A good synopsis on many aspects of argumentation. Pretty much stuff I already knew, but presented in a more formalized manner.

    Revival by Stephen King. I enjoyed it when I read it, but frankly can't remember what happens at the end. That kind of tells me something.

    The Defenders of Shannara: The Darkling Child by Terry Brooks. A good follow up to The High Druid's Blade, but suffers from a 'more of the same' vibe.

B+     Nemesis Game by James S.A. Corey. Unlike Cibola Burns, Nemesis Game returns to some of the original plot themes of the earlier books, conflict between earthers, martians, and belters. Overall an engrossing story.

    Gotham Central Book 1: In the Line of Duty by Greg Rucka, Ed Brubaker, Michael Lark. A police procedural in a world of super-heroes and super-villians. Interesting take and perspective. Decent characters, look forward to the others in this series.

    Wastelands 2 edited by John Joseph Adams. Again some good, some less good. Mostly good though. I thought the first volume of Wastelands was much better overall.

B+    The Golden Son by Pierce Brown. I like this world, but it is not new now. Still the story moves along well and ends in dramatic fashion. Looking forward to the last in this a good way.

    Inferno by Dan Brown. I liked it better the first time I read it when it was called the Da Vinci code.

B     Neuromancer by William Gibson. I liked this book, but not sure why it is considered such a great story. Probably it's a contest thing. Stories in this genre are more common than when Neuromancer was written.

    The Belgariad vol 2 by David Eddings. Read this many many years ago too. Also, a fun read but it wraps up a little too neatly.

B+    The Belgariad vol 1 by David Eddings. Read this many many years ago. A fun read, though there may be some sentimental value associated with my score. 

     How the Mind Works by Steven Pinker. Outstanding book on the brain and the work that has gone on into understanding how it works...or doesn't. Particularly interesting for me after the seizures of 2014 and thinking about the recovery process.

    Jingo by Terry Pratchett. Witty and good satire, but does not hold up as well to other Pratchett stories.

    The Defenders of Shannara: The High Druid's Blade by Terry Brooks. I enjoy Brooks a lot, again probably some sentimental effect here. But I have found much of his recent work to be somewhat predictable, different characters, different settings (within the Shannara world) but ultimately the same arcs occurring with the same pacing. The focus on a Leah descendant and the entwined story of Arcannen mixed things up enough that this book was a pleasant surprise.

     Parasite by Mira Grant. Great take on the zombie genre!

     Red Rising by Pierce Brown. Interesting Sci-Fi story dealing with class and revolution. Part one of ?.

A      Crossed Blades by Kelly McCullough. Introduction of Jax and greater development of the universe McCullough is creating. Look forward the remainder of the series, though I needed to read some other books. Characters are flawed yet heroic.

B-     Devil in the White City by Erik Larson. Two good historical stories that I liked but did not think wove together well.

     Cibola Burn by James S. A. Corey. I enjoy The Expanse series immensely, though I usually do not enjoy space related sci-fi. Great story that deviates from the previous three in plot.

    Bared Blade by Kelly McCullough. Another good read of Aral and Triss (Aral's shadow familiar). Further development of the McCullough's world.

    Broken Blade by Kelly McCullough. This world reminds me much of the Thieves' World universe. Although there is more diversity of culture, much of the story takes place in a Sanctuary-like city of Tien. (At least as how I recall Sanctuary after 25+ years.) Fun story, great character in Aral.

    I Killed Pink Floyd's Pig by Beau Phillips. Humorous stories of many of my favorite bands. Enough diversity in the types of things from drunken hotel room destruction to the title of the book that is stays fresh throughout.

34 books this year, although some will consider the 5 graphic novels as not counting but fuck 'em. Of the 34 books: 29 were fiction for fun,  2 were on the music industry/biography, 1 was philosophy, 1 was history (although not academic), and 1 was science.

New Student Posts en route

As Thanksgiving is over and another semester winds down, a time of great celebration is soon to be upon us. By which I mean student blog posts from my Eukaryotic Microbiology course! As I await the submission of the final drafts to roll in, I discovered some older posts in a folder that never made it onto Traveling Small with a Nucleus. So look through some of the older ones or check those that were not previously posted until now. Feel free to leave a comment or two for the students!

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:

    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.