Saturday, December 24, 2016

Happy Luxmas to All!

It has been quite a year, rich with ups and downs.  I'm not alone in that evaluation, I realize.

The death of my father in April gave me quite a bit to think about. Having my promotion file to full professor tabled early on was disappointing, but I think I need to be philosophical:  I will always have a, um, nonlinear path in academia.  

I'm a bit unconventional.  Okay, I'm an oddball and don't fit in very well.  But at least I'm true to myself!  And I truly do care about science and my students.  Besides, lots of great people in the microbiology community have been very supportive and helpful. It'll be okay; tenure is a wonderful thing.  

Lots of good things happened, too.  First and foremost, that fabulous family of mine:  my lovely and brilliant wife Jennifer Quinn, and my musical and smart and happy F1s, Anson and Zach. They remain the center of my universe.

I was elected to be Chair-elect for the American Society for Microbiology's Division W on Education, attended four microbiology meetings, ran a session on Art and Microbiology at the ASM General Meeting, ran a luminous art session at ASMCUE, published three book reviews and an essay.  I visited the American Museum of Natural History (and got a personal tour of the Microbiome exhibit!) and traveled to Amsterdam to see the microbiology museum Micropia and the home of microbiology, Delft.  I continue to have fun with students in my classes and my undergraduate research laboratory.  

But for all kinds of reasons, it's nice to see 2016 start to fade into the distance.

As always, some #Luxmas fun.

First, I have always adored tardigrades.  So I had a number of small 3D printed models made, and my wife and created a #TardiMas tree!

I played a bit with Serratia and GFP expressing E. coli.

Then it was, as usual, time for words on Petri dishes, painting with luminous Photobacterium leignothi.

That last really made me sad; I had wanted to write a parody of "White Christmas" on Petri dishes, and I just can't work finely enough to write:

I'm dreaming of a bright Luxmas 
Just like microbes that used to glow 
Where Euprymna glisten and quorums listen
To homoserine lactones in the crypt

I'm dreaming of a bright Luxmas 
With every Luxmas plate I swab 
May your genes be autoinduced, and bright
And may all your Luxmases make light!  
 Maybe next year.

Even a decent #LuxSelfie, reminding everyone (and myself) to look for light, even in dark places, during 2017.

And as always, my wife's beautiful #Luxmas tree video.

Enjoy friends and family this evening, and to the New Year.

Thanks for reading, and I can't wait to share more thoughts about microbiology, education, and life in 2017!

Thursday, December 8, 2016

Microbiology, Student Learning, and Creative Extra Credit

For a number of years now, I have been interested in exploring unusual strategies to promote ownership from my students in the classes I teach.  I find that lists of facts, conceptual maps, frequent assessment, group work...all of these have positives and negatives. But the real spark, I believe, is getting the students to become engaged in topics because of the choices they make---to "own" their work.

One approach I have tried is via the time-honored inducement of "extra credit." Students always pay attention to those words as well they should. But I add to it "creative projects."  

Thus, for that precious precious extra credit, I tell students to come up with a creative form of extra credit that is relevant to the concepts we have been discussing in lecture and laboratory.  

I scaffold the assignment in the following fashion.  First, the students need to get my verbal approval of an idea for their project. In this way, I can keep the project reasonable, topical to class, and not a "time-sink" that will take away from their other classroom responsibilities.  After two weeks, I have them turn in a one page description of their project, and justify it in terms of topics we have covered in lecture.  Again, this helps me make certain the projects are reasonable, topical, and helpful to the students.  The students also think more deeply about their projects.  Finally, at the end of the semester,  students turn in the projects.

And the results are gratifying.  

Here is Juniper's artistic interpretation of Carl Woese's greatest discovery.  I turned the pages she wrote and illustrated into a video, and added some jazz music in honor of Brother Carl.

Erin created a Bacterial Phylogeny of Many Colors.

Mara created a mobile depicting the human microbiome.

Carly and Anne made #MicrobialCookies (and wrote a long "key" to explain each choice).  Always a crowd pleaser.

Makenzie created a knit phage that fit inside a knit bacterium.

Renee created a flip book that shows how the Type 3 Secretory System is assembled.

Emily created a paper mache mobile of microbial wonders.  A phage wearing a Santa hat can never, ever be wrong.

Kyle adapted "My Shot" from the play "Hamilton" to the armament wielded by Vibrio cholera's Type 6 Secretory System.

Austin made very intricate shadow boxes displaying the different parts of the bacterial cell wall.

Josh painted an epic bacteriophage.

Cooper wrote a short-short story, in the style of Edgar Allan Poe (or as he put it, "Poe-karyote"), about the endosymbiotic model of eukaryotic cell evolution.

Jesse created a plush Euprymna scolopes, complete with remote controlled LED lighting to represent Vibrio fischeri in that wondrous symbiotic relationship.

Trini drew various microbes as "Micro-Avengers."

Anna decided to adapt Taylor Swift's "Shake It Off" to "Plate It Out."  Complete with, yes,  backup dancers.

Molly cross stitched one of my favorite sayings that reminds me of Pasteur's famous line:  "In the end, the microbes will have the last word."


I have found that some educators shrug at this approach, or think it is trivial.  I respectfully disagree.  There are many roads to learning, and teaching, effectively; we spend a great deal of time judging and less time listening, in my opinion.

What I do know is that my students---my micronauts---enjoy this kind of assignment, and learn a great deal from it.

One further thing, something that may be the most important point of all.  Year after year, a quiet student will tell me that she or he lacks any kind of talent.  Then, I discover that they can sing well, dance, draw, paint, write poetry....and the look on their faces when fellow students (and I) applaud their project is worth it all.

Tuesday, December 6, 2016

The Coolest Thing Bio350 Micronauts Learned in Fall 2016

Well, it is the last day of my beloved microbiology course, Biology 350, here at the University of Puget Sound.

Because there is just so much #OMG (overwhelming microbial greatness) to share, I always remain conflicted at the end of each Fall semester.  Did I give good coverage of the material?  Did I leave out anything important?  What can I do better next time? What new concepts MUST be in the next iteration of my course?

Truly a moving target.

So on the last day,  I try to have my brave micronauts tell me the single "coolest" thing that they have learned in my class.  Here is a video with the thoughts of my wonderful micronauts from this semester.

What can I say?  You might say that they now "see" through "microbe colored glasses."  Or that they all drank "the microbial Kool-ade" (as I have been accused to microbially propagandizing students more than once).  

I often talk about the #OneTrueMicrobialFaith.  We do need to promote what I have long called "Microbial Supremacy."

Artwork by the great Kaitlin Reiss
Yes, I think that there needs to be MUCH more microbiology, MUCH earlier in EVERY biology curriculum.  But that gets me called names.  Still, as the saying goes, I didn't choose the bug life; the bug life chose me.  

I remain a proud and unrepentant #MicrobialSupremacist.

My students this semester? I like to think that they now have a new perspective of the primacy of the microbial world, from the bottom of the ocean (and beneath the crust) to high in the atmosphere (and perhaps beyond).  

First evolved, and last extinct, indeed.  

So my micronauts have a whole new way of perceiving not just biology, but the world around them.  I hope that they can take that knowledge and perspective into other classes, and after graduation into their next venture.

It's a privilege working with students here in Tacoma.  It's an honor to watching budding micronauts develop!

No semester is perfect, and there were some real challenges for me outside the classroom and laboratory this semester. But I think I got the #MicrobialPoint across!

Sunday, November 27, 2016

Tests, Brave Micronauts, and Educational Art!

One of the things that I never believed as a student lo these many years ago was that professors didn't like giving examinations, and didn't feel that your score really "measured" your worth or abilities as a student.

On the other side of the lectern, I am here to tell you that it is very true:  we don't enjoy giving exams (well, and we enjoy grading them even less).  We indeed don't think a student's performance on a test measures much other than how much they studied.

When my sons were younger, I would ask them what a test was intended to measure.

"What you learned in class?" they promptly replied.

But that would be a long, long test, I reminded my sons (and I remind my students of that when they ask).  All a test really does, friends and neighbors, is measure how hard you studied consistently.  That is a valuable measure, but imperfect.

Over the years, I have found that students learn best when there exists ownership on their part.  The student selects the term paper topic.  The student comes up with a challenging question.   Ownership works.

In my Fall semester Microbiology course here at the University of Puget Sound, I have seventeen brave micronauts to whom I preach the One True Microbial Faith™.

Test times can be challenging.  First, I have a mascot (from Micropia, the microbiology museum in Amsterdam) encouraging them.

Next, I feed them.  Too much grease from McDonald's hash browns this time, I suspect. But they are young, and have remarkable metabolisms.

I then hand out "Comfort Microbes" from GiantMicrobes to relax the students during test taking.

Emily with MRSA
Juniper cuddles up to Chlamydia
Carly gets to know Campylobacter
Anne lives tough with a tardigrade pillow.

Renee and the Zika virus have a special moment
Erin gently holds an old student made Bdellovibrio, which is now sadly falling apart.

Trini and Salmonella were meant for each other.
Molly and staphylococcus seem of one mind.

Josh and his Treponema get to work (sssh---don't call Treponema syphilis)

On this exam, I asked my micronauts to illustrate with a cartoon (and hopefully some humor) one of the concepts we discussed in class since the first exam.  In the past, I have found this approach has interesting effects:  it encourages deep and integrative thinking, the "new" approach shakes up the student brain, and I learn fascinating insights into my class, and the student mind.

Here is what my micronauts came up with on Exam #2.  Enjoy!

One of the concepts I repeated many times during the "microbial metabolism" portion of my course is the role that precursor metabolites play.  PMs are the "common metabolic language" all living things "speak."

Recently in class, my I discussed with my micronauts the idea from Carl Zimmer's fine essay "The Human Lake" that we humans are a series of ecological niches in which microbes can adapt and prosper.  Walking ecologies, we are!

Thought we didn't have a lot of time to discuss it, I always enjoy telling students about giruses in general, and in particular the discovery of the mimiviruses, including the origin of their name as microbe mimicking viruses!  Viruses with more DNA than many bacteria, and visible under the light microscope...well, it helps micronauts see that my beloved microbiology is not simple!

During my short sessions on virology, I do speak a bit about influenza.  The concept of antigenic shift seems to stay with students effectively.

Now this one was interesting!  The cartoon is based on phenotypic complementation/synergism observed in our lab when two Serratia marcescens mutants blocked at different steps of prodigiosin synthesis are streaked near to one another.

We see this phenomenon each year during the genetics portion of the microbiology lab, and students always find it pretty interesting.

So the cartoon makes sense.  Including the "prodiawesome" pun.

I often tell my micronauts to think about gene regulation of the organisms in our gut---expression of various catabolic genes must change quickly during our meals.  So here we go from being "hangry" to being well-regulated!

Speaking of regulation, the way negative regulation of the tryptophan operon in E. coli works reminded one student of the relationship between TrpR and the co-repressor tryptophan.

The Rainey and Travisano paper showing "adaptive radiation" of Pseudomonas syringae in small glass tubes is a conceptual winner, year after year.  The Hand of Darwin is on us all, and evolution can take place during cultivation of bacteria!  

This led one of my students to, um, some dark places.

We also discussed how horizontal gene transfer impacted interactive and operational genes during lecture.  The concept was on the following student's mind!

I was very glad to see that at least one student shared my fascination with riboswitches.  Adding cis and trans effects to the mix only made me happier. 

I consider Rubisco and nitrogenase to be the two most important enzymes on the planet (fixing carbon and fixing nitrogen).  In this cartoon, the student links the course paradigm of compartmentalization to the toxic effects of oxygen on nitrogenase. In this case, a heterocyst from a cyanobacterium mixed in with a bit of Harry Potter! 

When I teach my micronauts about precursor metabolites, I remind them that when we eat a steak, we don't just plop the steak onto our arms and have it fuse muscle tissue to muscle tissue.  Instead, we break down the steak to protein to amino acids, and then build things up again with that common metabolic language of PMs.  

This clearly had an impact on one student, in a holiday relevant fashion.

No exam can cover every topic discussed during lecture (nor would any student want to take such an exam!).  So I was quite pleased with this one.  At one point during the evolution portion of the course, I had the students read a bit about the elusive Lokiarchaeta, which may be the ancestor of every eukaryotic cell. One reason, according to the reading, was the presumptive flexibility of the cell membrane, allowing this early cell to carry out endocytosis (something there is little evidence for among bacteria and archaea). But endocytosis is absolutely necessary for the modern eukaryotic cell, with mitochondria and chloroplasts; it is the centerpiece of the endosymbiotic theory of cellular evolution.

So this student gave a "Jaws"-like thematic view of this ancient, ancient possible ancestor.

When I discussed virology with my micronauts, I did spend some time on influenza.  And the characteristics of the virus that make genetic drift and shift possible are fascinating.    Note how this student does a nice job illustrating how a progeny virus can end up with a "reassorted" segmented RNA genome!  This is, in fact, the basis of genetic shift in influenza.

The concept of the Type Six Secretory System acting like a spear or stiletto to kill or inhibit other bacteria remains fascinating to students, as you can see.

The last cartoon from my micronauts is a bit personal.  Microbial taxonomy is a strange field of study, only recently finding a basis using molecular chronometers.  In the past, it was solely based on phenotypes.  And not all phenotypes are created equal!

In graduate school, I worked a bit with Rhizobium meliloti, which induces nitrogen fixing root nodules on alfalfa plants.  My PhD advisor, as a postdoc, had made mutants of R. meliloti that could not form nodules---making it possible to "fish out" genes responsible for that complex and fascinating symbiotic phenotype.

The story goes that, as my advisor was giving a seminar on this topic, an extremely venerable microbiologist interrupted.  He insisted that the mutant bacterium was no longer Rhizobium meliloti.

Certainly, based on DNA, it was.  But the venerable microbiologist insisted that the definition of Rhizobium meliloti was "that which nodulates alfalfa."


I use this story to illustrate the dangers of trusting in any one phenotype.  And I think the story "stuck"!

I continue to think that this "cartoon" approach to learning has its place.  Consider adding it to your armory of educational tools! Truly, ownership is central to student learning; this can help.

Plus, I am proud of my micronauts and wanted to show off their wit and wisdom.

Monday, November 21, 2016

Biology 350 "Nanobiographies" by my Proud Micronauts!

One of the problems I face here at the University of Puget Sound is what I call the "N=1" issue.  There is only one microbiology class!

Thought it is true that I strongly believe that microbiology should "Occupy the Curriculum"----

----I still have to deal with the single course in microbiology we have available to our undergraduate students.  I do my best to turn them into enthusiastic micronauts in the one semester we have available.  Here is my current class of #Bio350 micronauts.

One way to do that is to give the students an opportunity to really delve deeply into a specific microbiological subject.  There is, after all, so much to microbiology overall (especially in a one semester course).

In my course, we don't call them term papers.  We call them "Microbiographies."  And as part of this assignment, I encourage my micronauts to create one page summaries of their topic, written for a non-science audience (such as nonscientist parents or friends in other majors).  Since these summaries are only one page long, it is natural that I call them "Nanobiographies"!

Please enjoy the Nanobiographies written by my hard working micronauts of Biology 350 in the Fall of 2016.

Renee became fascinated by Type III Secretory Systems.

Carly became intrigued by the idea of using bacteria to fight cancer directly.
Juniper explored a very, very hostile environment on Earth, despite an amusing name:  snottites and acid biofilms.
Austin, with his interest in dentistry, wrote about the OG of the cariogenic world, Streptococcus mutans.
 Mara quickly became entranced by the wonders of Wolbachia.
Makenzie explored a common food born pathogen, Listeria.
Jesse decided to shine a light on the archetypal squid-Vibrio symbiosis, with a bit of Harry Potter thrown in.
 Trini explored the possibility that gut microbes could impact human behavior.
Molly wrote about the central issue of how we obtain our microbiota at birth.
 Emily, interested in life on other planets, decided to write about SLiMEs, which could easily be found on other worlds.
Kyle enjoyed writing about some microbes can generate electricity.
Anna, with her deep interest in marine biology, explored the relationship between microbes and coral.
Brennan wrote about Streptococcus pyogenes, one of several "flesh eating" bacteria.
An avid swimmer, Anne wondered about what microbes could join us in the pool!
It's true that Josh went there:  fecal transplants.  No wonder "South Park" is involved.
Erin became interested in the role that human microbiota might have on cancer treatment in general.
Cooper decided to delve into the scary world of MRSA.

I find that when students select their own topics, there is more "ownership" of the assignment.  It certainly seems that way when I look over the interesting Nanobiographies written by my current crop of #Bio350 micronauts.

I hope you enjoyed their essays, as well.