A Hiatus...and Rules in Academia...

So, yes, it has been a while since I posted on my blog. Apologies all around, and I will try to post much more frequently.  

Soon after the end of my Microbiology class last semester, my father became quite ill.  I have been quite worried about him since the death of my mother in October; his hospitalization and long convalescence made me fear the worst.  My father is strong and wise, but is not young.  After quite a scare, my father is better now---which is very good news.   

As the new semester dawned, I had a large freshman course with which to deal.   My large course, with 48 students (which is not large by RO1 standards, I realize) is a bit of an adjustment; I had not handled the logistics (grading, primarily) of that number of students in some time at Puget Sound.  But I am starting to catch up! 

To that end, a quick post, about life in academia, and some “rules” for research with students.

Over the years, I have made so many mistakes as I progressed through academia that I cringe a little, remembering.  I don't have a time machine to go fix anything, but I have learned a few lessons.  Thus, I have some "rules for research" and I also have some information from a former colleague of my wife's at UW-Tacoma to share.

The rules are not necessarily complete, nor do they necessarily apply to everyone reading this.  Still, I think it is important for any academic to think about these rules, and maybe to pass them along to other academics or folks considering a career in academia.  So I thought I would share them.

First, something from my wife's colleague at UW-Tacoma (Beth Rushing, Former Vice Chancellor for Academic Affairs).

"Five Things I Wished I Had Known When I Was Beginning as a Faculty Member"

1.  There is a hierarchy among faculty members.  Respect it.

2.  You can be friendly with students, but they are not your friends.

3.  Sometimes you have to say "no," close the office door, and/or work at home.

4.  Everyone's job is important. Be nice to the staff in your program.

5.  Your job is not your life.

These rules are perceptive and true.  #2 always cuts me to the quick.  It is true that some students can become friends, but not initially. If I were to add anything to this list it would be simple:  stand by your ideals in a calm fashion.  We all have trouble with disagreements; learning how to be civil about dissent is important.  Avoiding disagreements does not help (as I have learned to my sorrow repeatedly).  Also, there is a difference between honesty and tactlessness; many people confuse the two. 

I like Dr. Rushing's rules.

Even though I am not working at a PhD (or MS) granting institution, and only do research with undergraduate students, I have worked with a few.  I have sent about 14 of my serious undergraduate research students off to PhD programs, so I have some experience with the joys and sorrows of research at primarily undergraduate institutions.  So here are my “rules.”

"Martin's Rules of Research"

Rule #1:  There is one ego per lab (and it isn't yours).

Rule #2:  Research projects sometimes appear to actively resist investigation (I take it a little personally).

Rule #3:  Never forget that there is a "re" in the word "research."  If you cannot repeat the experiment, it isn't science.

I teach all of my students these rules, and I have plaques with #2 and #3 up in lab. 

Rule #1 is amusing to me.  Few undergraduates laugh when they hear it, but everyone with a PhD does!  I know I have seen people get into real trouble forgetting #1, and I have struggled myself with it.  It’s not a “the PI is God” kind of concept.  It is a reminder that none of us “own” our research projects! 
  

Rule #2 has certainly seemed true to me, over and over again as I work with "undomesticated" microbes.  It's like the microbes are snickering at me on plates and in 2059 tubes, when I turn my back.  Fair enough:  it just makes me more determined!  And Rule #3 is a great, great thing for students to remember.  I well remember a former student getting a tricky enzyme assay to work.  "Did it!," she exclaimed.  "Great," I replied.  "Now do it three more times."  The student was confused at first!  But the ability to repeat an experiment successfully (with different hands) is at the core of good science, in my opinion.

My rules are all based on painful yet instructive lessons from my own life in academia.  Everyone is different, of course.  You know the saying:  YMMV (your mileage may vary)!

Thoughts from My Class on Small Things Considered!

Here is a quick post, while I am trying to learn some bioinformatics at Argonne National Lab.  

My thoughts about teaching microbiology at a small liberal arts institution, and what some of my students thought about microbiology, appeared today in the ASM sponsored microbiology blog, "Small Things Considered."  I hope that the post gives a flavor of the kind of classroom I try to create, and the experiences my students hopefully gain.

You can read the essay here.

An Inspirational Note Worth Reading: Grace in Teaching!

Teaching has its ups and downs, like any other profession.  It's a great feeling when a struggling student does well in class, and shows the excitement we try to teach regarding a theme or concept.  It can be sad when course evaluations suggest that the class isn't "getting" what you had intended and we need to retool our approaches (leaving aside the less-mature commentary that happens from time to time).  And, recent magazine articles to the contrary, most educators work quite hard to do the best job we can for our students (there was quite a bit of bemusement and a bit of sarcasm regarding the silly article in Forbes, such as here and here).  Doing a good job for our students remains a moving target, even for the best of educators.  We tell ourselves that that it matters, that it is worth it.  And many of us---yours truly, for example---find it to be very much worth the time-equity investment.

But it is always good to read something inspirational about teaching, that presents new approaches, and perhaps more importantly, a new outlook.  

A colleague of my wife's, Dr. Francis Su of Harvey Mudd College, was just presented the Haimo Teaching Award at the Joint Math Meetings of the Mathematics Association of America last week.  It is a great honor to receive a Haimo Award (full disclosure:  my wife won this award several years ago...and yes, I married up).  Dr. Su's acceptance speech was remarkable.  It deeply moved my wife, and she sent me a link to the speech.  I could see what she meant!  

Dr. Su posted the acceptance speech on Facebook, and I share it with you here:

Click here to read Dr. Su's wonderful acceptance speech.

Note:  Apparently, Facebook took down Dr. Su's post as spam(!).  No matter; Dr. Su kindly created a website with his talk for us all to appreciate.  I changed the link above so that it will take you to his new website.  Apologies for Facebook's, um, attention to spam.

If you are an educator, or a student, or interested in teaching or learning, please read this speech.  It is on the subject of "grace" in teaching, learning, and growing.

Richly deserved applause to Dr. Su...and not simply for the prestigious Haimo Award.  But for being willing to share his outlook and positivity with all of us.  

His students must be very, very lucky!

Educators and students:  consider the grace in your life.  And increase it with others.

More about Microbial Literacy!

Just a quick post.  I have long believed that microbiology needs to be presented in the Biology curriculum, earlier and in more detail.  It's fundamental. And I find that the typical media (as opposed to science journalists and bloggers) in particular can really confuse things revolving around microbiology, and that isn't good for education or the public at large. 

A student from last semester's microbiology course sent me a link to this video, a promotional spot about Boise State University, shown during a football game.  

I was delighted to hear the young woman mention that Boise State, to her, could mean "quorum sensing."  Fantastic!

But then, I read the press release that mentions that spot, and its "shout out" to Microbial Goodness.  I put my head in my hands:

"Quorum sensing is a system of stimulus and response correlated to population density.  The Department of Chemistry uses it to study bacteria such as the West Nile virus in its research work on viral vaccines."

Oh, my.  West Nile virus, of course, is emphatically not a bacterium.  So I went to my good friend Google.

I believe that the promotional spot is referring to Dr. Kenneth Cornell at Boise State University.  His research covers quite a bit of ground, but he does study quorum sensing in some of his research, and also is involved in working on a West Nile vaccine.  Somehow, these two items became linked by the PR department?

It's common to read, in everyday media, the confusion between "bacteria" and "viruses."  So it is important to push for "Microbial Literacy."  This is a good example:  the well-intentioned effort to promote science was laudable, but the details were incorrect.

So I urge public relations offices producing these kind of spots to check their work carefully, so that their hard work will have the intended effect:  helping the public to see the value of science in their everyday lives.

A Sad Post: RIP Carl Woese!

I just returned from a quick family trip, to continue finalizing grades from my Fall Microbiology course.  I logged onto Twitter, and received the news I had been dreading for some time now.

Carl Woese has passed away.

84 is a long life, and it was well lived.  But pancreatic cancer is an awful disease (it took another hero of mine, Randy Pausch, years ago).  So once I heard that diagnosis, I knew that the outcome was seldom positive.  At the same time, Woese did some remarkable things during his life, and the world is a poorer place without his example and polite refusal to intellectually "knuckle under" to convention or criticism (watch his video interview from 1998, linked below, and you will see what I mean:  polite, driven, and devoted to the data).  There is a saying that change can be evolutionary or revolutionary; the former is slow, while the latter is often bloody.  It's also true in science, and in some ways, Carl Woese experienced both.

A quick glance at the entry in Wikipedia for Carl Woese shows that he had been honored with every major award a microbiologist could receive, short of the Nobel Prize.  And many people, myself included, felt his contributions were sufficient to merit that recognition as well.  Two eloquent voices I can point to on this topic are an editorial by Nature Reviews in Microbiology here, and Jon Eisen's well-reasoned essay here.

Woese is one of the names that I insist my students know and respect---not just in my microbiology course, but in my introductory cell and molecular biology course.  And it is not simply about the Tree of Life, central and wildly important that it is to biology.  It's also about the path to acceptance of the data that Carl Woese collected, and how he personally walked that path.

Woese's (and his coworkers') insight that the archaea are as different from bacteria as bacteria are different from eukaryotes, was fundamental, and not universally accepted at first.  In fact, Woese experienced several eminent scientists disagree with him quite forcefully regarding the Three Domains model, including  Salvador Luria and the formidable Ernst Mayr.  The long term disagreement between some of these scientists and Woese was not altogether professional from time to time, and that aspect of the paradigm shift clearly had an effect on Woese.  When I met Carl Woese at Woods Hole in the late 1990s, and burbled on enthusiastically about his work, he was polite but distant.  Given what happened to him during that period of time, who could blame him?

Still, I am reminded of J.B.S. Haldane's waggish but too-often sadly  accurate description (page 464) of how science progresses, in stages:

"Theories have four stages of acceptance.  i) this is worthless nonsense; ii) this is an interesting, but perverse, point of view; iii) this is true, but quite unimportant; iv) I have always said so."

A former undergraduate student of mine, Micheline Wong, actually added a fifth stage:  "And I came up with the idea first."  She was awfully young to be that cynical, but Micheline was not wrong; I have seen that "evolution" occur among scientists several times over the years.

So I deeply admire Carl Woese's work, and the philosophy and unwavering drive behind that work.  Like Peter Mitchell and Lynn Margulis, Woese had an idea, and the data to back it up.  When resistance was encountered, he just continued to work, filling in gaps, and evaluated each data set as he collected it. It is true that Margulis and Mitchell, from time to time, would advance, um, unusual ideas.  But that never took away from their great accomplishments, I would contend:  the chemiosmotic theory of bioenergetics is awfully important to all of biology, as are the endosymbiotic orgins of mitochondria and chloroplasts.  In a similar fashion, Carl Woese had some iconoclastic ideas about what he called "pre-Darwinian" evolution.  Based on his track record, I tend to think very, very carefully about anything that Carl Woese wrote; his insights are unique.

I would also like to draw your attention to Jon Eisen's analysis of Woese's original journal articles that explored the possibility of a Third Domain of life:  the archaea.  Eisen believes that the 1977 article by Woese may be one of the most important papers in the history of microbiology, and I can see his point.  Read his essay over and see if you agree.

Let me be clear for a moment:  I don't feed at a high trophic level in science; I am mostly an educator who dabbles a bit in research with undergraduates (and tries to groom such students for PhD programs).  There will be far more eloquent and wiser heads than mine eulogizing this remarkable man's contribution to the biological sciences.  But I cannot emphasize the centrality of the paradigm shift the work of Carl Woese created:  it has fundamentally changed the way we looked at the relationships between all living things.  And in so doing, it created the backdrop necessary for so much of the current furious ferment in microbiology.

But please don't take my word for it.  Quite a while ago (14 years!), the American Society for Microbiology and the Public Broadcasting Service (along with the Department of Energy and National Science Foundation) put together a genuinely great video series about microbiology.  I assign various segments of this series to my microbiology students each year.  The series title "Intimate Strangers," the Enya-style soundtrack, and unfortunately near-soporific narration, sometimes make my students roll their eyes when they think I am not looking. But in particular, I have them watch, and we discuss, the segment detailing the contributions that Carl Woese has made to biology.

You can view the video here.  There are wonderful comments and insights given by Norman Pace, as well as Carl Woese himself, who describes how he went about creating the data set which turned into the Tree of Life (and how he felt about doing so---the all-encompassing drive to complete the puzzle).  Even the irrepressibly enthusiastic Karl Stetter speaks out.  Norm Pace, at one point, opines that Carl Woese has done as much for the study of biology as Charles Darwin.  

Personally, I think there is a case to be made for this point of view.  Perhaps not many biologists think so now.  But change is sometimes, as I wrote above, evolutionary.  My money is on Carl Woese, as usual.

A final note.  In last semester's Microbiology course, Carl Woese came up several times.

First, in a lovely "woolen sculpture" by Amy Wright of Carl Woese from an iconic photograph, along with a miniature blackboard complete with the Tree of Life.  In the back is my favorite quote from Pliny the Elder.  Roughly translated, it reads "Nature is to be found in Her entirety nowhere more than in Her smallest creatures."). 

Second, Carl Woese appeared as a portrait "painted" with luminous bacteria (by my wife Jennifer Quinn) as part of my Microbial Hallowe'en this year:  

And finally, on Hallowe'en proper, a student came to class dressed as Carl Woese (the other student is trying to look like another Microbial Hero™ of mine, C.B. van Niel).

So I think about the world of microbiology without Carl Woese, and I am sad.  But I am reminded of the following passage, from the late Ray Bradbury's novel, Fahrenheit 451:

"Everyone must leave something behind when he dies...Something your hand touched some way so that your soul has somewhere to go when you die...It doesn't matter what you do, so long as you change something from the way it was before you touched it into something that's like you after you take your hands away."

So for me, I think about Carl Woese looking at the Five Kingdoms and other early taxonomic plans.  And then I begin thinking about how he started puzzling together those spots of radioactive fragments of 16s rRNA on the autorads, assembling them by hand, bit by bit, into the Tree of Life with the Three Domains we all see today.

I will see Carl Woese's face in the metaphoric bark of that Three Domain Tree of Life, every time I look at it.  I will see his face every time I teach it.  I will make sure that my students see his face, too.  

And to change the way we think about how all life is related is a fundamental, remarkable, and lasting legacy indeed.

Condolences to his family, friends, and colleagues.    

Have A Happy Microbial Holiday Season!

As I begin to assess last semester's Microbiology course (and continue to grade final exams and independent project reports), it might be a good idea to reflect upon the coming holiday season...and (of course) relate it to my beloved microbiology!

There have been many "holiday themed" microbiological images and themes on the Internet of late, including Giant Microbes, poems, cookies, and a nice report from 2008 of microbes within and helping to form snowflakes.  Even these beautiful "frost flowers" have at their core the Small Masters that rule our macroscopic world.

Source:  National Geographic link above

As I cruise across the Internet this time of year, I have seen other holiday themed Microbial Goodness™, including this fungal Christmas Tree.

Source at the link

The cell biologists and microscopists become very creative this time of year (the Holiday Cheer / Ethanol Extractions?), and make things like this lovely "microbial wreath" using fluorescent dyes and optical manipulation (the extremely skilled Donna Stolz of the University of Pittsburg put this beauty together!).

Source at the link above

And on FaceBook, I have seen some "homegrown" attempts to bring the holiday spirit to the research lab, as can be seen below (and yes, I am very jealous my own research students didn't make these!).

Folks in this lab were certainly "handy"!

I guess this is a "Tipmas" tree?

But here in my home, my long suffering wife and children allow there to be a Microbial Tree (and yes, I have it up year round, though the bioluminescence doesn't last very long!):

Some of the ornaments are indeed "painted" with bioluminescent bacteria.  But in the light, you can see several items of interest.

There is a bacteriophage "top" to the Microbial Tree (courtesy of Giant Microbes).

And a closeup shows more Giant Microbes goodness, along with Michele Banks' (artologica on Etsy) wonderful microbially-inspired ornaments.

Yes, I am obsessed.  But I simply blame it on my microbiota which are clearly manipulating my behavior (or so I say whenever asked).

But it isn't just me.  Last year, my talented and extraordinarily patient wife Jennifer Quinn pulled out all the stops.  Based on a series of photographs I took of the "Luxmas Tree" with different light levels, she created a "movie" for you to enjoy.

Click here for the movie.

In the next couple of weeks, I will post more about my Microbiology course last semester (I still need to write about their independent projects, and the last day of class), my Introduction to Cell and Molecular Biology course due to start this Spring semester, and even information about my undergraduate research program.  

But for now....may your days be microbially merry, and bioluminescently bright...and may all your holidays be white with bacterial-generated snowflakes!  Happy holidays!

Student-Centered Learning, Part I: Nanobiographies!

It's been a while longer than I had hoped since my last blog entry.  A second exam, a quick trip to a microbiology conference (where one of my research students presented and did a fantastic job), and the like, interfered.  In any event, my beloved Microbiology course is winding toward a close, after a wonderful semester.  I learn as much, if not more, from my students than they from me---and this year was no exception.  I have many ideas, based on what I have gleaned from this crop of Micronauts, that I am looking forward to implementing in the Fall of 2013.  Next stop, my cumulative Final Exam.

One of the challenges in teaching any kind of broad yet deep topic, like Microbiology, is how best to navigate the vagaries of student learning.  Let's face facts:  tests are but one measure of what students "get" from a course, and often not a very accurate one.  Student "learning styles" are genuinely variable.   Thus, I like to give students an opportunity to investigate a subject for themselves; I find that many students "bloom" with such assignments.

Enter the ancient concept of The Dreaded Term Paper™.  Being true to myself, I call such a paper a "Microbiography."  Students are asked, in a scaffolded fashion, to create an in-depth investigation of a microbial topic that interests them (I usually insist that they stay away from viruses, other than mimiviruses or bacteriophages, and generally stick to bacteria and archaea).  First, students obtain approval of the topic from me (and I share my thoughts on their topics).  Later, a one paragraph summary of their goals for the paper.  Still later, an annotated bibliography and an outline.  All of this leads up to the final product, which I direct and shape with a detailed rubric (so that the students know what I am hoping to see).  

The fact is, I have had a number of Microbiology students over the years win writing awards from our campus' Center for Teaching and Writing and Learning for these Microbiographies.  And it's not a surprise:  students pick a topic which genuinely interests them, the assignment is scaffolded (to prevent, or at least hinder, "last minute" jobs), and the expectations are clear.  This allows students to really dive into a topic, and not only learn a great deal...but provide others (including yours truly) with valuable insights into specialized microbial topics.

One of the later "scaffolded" assignments is a one page summary of their Microbiographies, which I predictably call a Nanobiography.  The goal, I tell my students, is to create a one page essay (with diagram or cartoon) explaining what is wild and wonderful about their particular topics.  The intended audience?  Their peers (or even their parents!).  Some students are businesslike.  Others highly creative.  But I would say that all students benefit from the assignment, and they enjoy reading about the fellow students' topics in such a format.   Thus, I thought I would share this year's Nanobiographies with the readers of this blog---from the students who didn't mind my posting their one-page essays here, in any event.  

It gives me a chance to brag about my students, after all!  

Below each of the titles you will see is a clickable image of the relevant Nanobiography.  Feel free to click and enjoy!  I hope you enjoy reading these as much as I did!

The Spiteful Cell:  Pyocins versus Cheaters!

Microbial Freeze Tag:  Life at Low Temperatures.

Compartments, Paradigms, and Carboxysomes.

Virophages:  Parasites of Parasites?

An Attractive Proposition:  Magnetotactic Bacteria.

Archaea in Sickness and in Health.

A Weighty Question:  Microbiota and Obesity.

The Microbial City on a Tooth:  Ecology of Dental Plaque.

Streptococcus thermophilus:  Farmer, Pharmacist, and Survivor.

Some Like It Hot:  Hyperthermophilic Microbes.

The Microbial Juggernaut:  HA and CA MRSA.

Squid for Rent:  All Microbial Applicants Must Glow.

Harnessing the Tiny Killers:  Bacteriophage Therapy Redux.

An Aggregate Heartbreaker:  Bacterial Endocarditis.

There is no "I" in Colony:  Social Shortcuts Among Microbes.

Cavity Creeps Who Are Bad to the Bone:  Porphyromonas gingivalis.

Septic Salivary Symbionts:  Oral Microbiota of Komodo Dragons.

Chatter Among Teeth:  Communication Among Dental Plaque Microbes.

Black Plague:  A Story of Subversion by Yersinia pestis.

What's (in) a Hoatzin?

Sugar, Spice, and Microbial Nice:  Microbes and Flavor in Chocolate.

These are remarkable students, and I will miss sharing Matters Microbial with them three days a week (plus lab sessions).  Fingers crossed for all of them during the upcoming Final Exam!