Tuesday, August 30, 2016

Students Impressions of "Microbiology" on the First Day of Class

I'm very fortunate to be able to teach microbiology every Fall semester at the University of Puget Sound---eleven years now!  I mostly have juniors and seniors, and there is only one microbiology course available.  Mine.

These are some serious microbiological shoes to fill.

I do my best to present to students the wild ferment (sorry about that) of near daily changes in the microbial sciences.  It's such fun to tell students, pretty much every day, something new and exciting that was not known five or ten years ago.

Anyway, I thought you might enjoy hearing what my budding micronauts think of the term "microbiology" on the first day of class.  

Truly, I am fortunate to have students like these, and more fortunate still to have such a wonderful job.  I'll remind myself of this when I am locked into Grading Jail later in the semester.

I am lucky.

Sunday, August 28, 2016

A Long Hiatus....

I haven't written a blog post since January of 2016.  It has been a difficult period for me, personally.  Yes, many people deal with far worse; I am simply explaining my absence from posting.

I will be posting again with regularity, but I had best explain recent events.

My mother, Wanda Jean Martin, passed away in 2012.  Her death was after a brave and valiant fourteen year fight with Stage IV ovarian cancer, and she stayed pretty sharp mentally until the very end.  That doesn't mean it was a wonderful experience for her, or for her family, of course.

It left a hole in our lives, of course, and nowhere more than in the heart of my father.

My father, Jack S. Martin, Sr., passed away at the end of March of 2016.  Dad had spent his entire adult life looking after my mother. His hard work, sharp wit, grim humor, and perseverance were proven tools that helped my father through a tough life; but they couldn't do much against my mother's cancer.  It was the first challenge he had ever faced he could not master.

After my mother passed away, my father's health declined rapidly. Even so, he was very, very strong.  The last two years, it broke my heart to see how his mind slowly but surely unraveled as his body began to fail him.  I am fairly certain my father had several strokes along the way, or oxygen deprivation.  He had good days and bad days.  I learned to put aside the latter, and savor the former.  I didn't even mind him repeating the same stories again and again; they gave him happiness and made me smile. 

There were bad times, too, during my father's slow decline. All we could do, as a family, is focus on the lucid and positive moments my father had.  And celebrate his many positive impacts on our lives.  Certainly, we could have focused on the darker end of things, the anger, the hallucinations, the dementia, and the harsh words. But I chose not to do so.  I learned a lot during the experience; mostly about the nature of love and family.  And memories.

Here is my father's obituary.  So strange to see such a rich and colorful life as mere words on a page.

The last month before my father died, I wrote short essays about the role he had played in my life:  lessons, humor, experiences.  I think I knew somehow his time had come.  I put together a slide show of the little essays here.

My father was an unusual and unforgettable man.  One thing he insisted he wanted at his funeral was bagpipe music.  It didn't happen, and that bothered me more than a little.  With my uncle and brother's help, I put together a slide show, in honor of my father's birthday in July.  My friend KT Scott provided the bagpipe music. Here it is.

Neither my father nor myself believe in coincidences.  So the fact that he was buried next to my mother, on what would have been her birthday, surprises me not at all.

Please read a little about my father.  And honor him with a Dos Equis, if you would.  

It is absolutely true that my father told me he had never felt like a man until his own father passed away.  Since my father was the toughest man I had ever met, this surprised me no end.  

But I know what he meant, now.

I have always adored Dylan Thomas' poetry.  Obviously, "Do Not Go Gentle Into That Good Night" is appropriate.  Here is a video of Thomas reading it.

Furthermore, another poem of Thomas', "And Death Shall Have No Dominion," moves me deeply as I think of my father. 

Both poems certainly apply to how I felt about my father, at the end of things.

Many thanks to my wife Jennifer Quinn for her support during this difficult time.  Also for my brother, Jack S. Martin, Jr.  And finally, my father's "little brother" and my uncle, George F.  Martin, for patiently and kindly keeping us all in one piece during this awful journey.

Hug your family, and call your loved ones.  Do it today.  Right now.

Thursday, January 28, 2016

Microbiology, Cartoons, and Take Home Lessons!

Yes, things are too busy as usual, with classes, grading, adolescent children, elderly family members, and slowly swimming upstreak. But over the break, I learned some interesting things to share with readers (I can't really tell if people read these posts, but thank you if you are doing so!). I hope that everyone had a good break, and have settled into the New Reality of 2016.

I have been clear on this blog that I appreciate different pedagogical approaches, and have observed that students learn in different ways---often relating best to their own skills or interests.  Recently, I have been exploring how artistic approaches by students can improve learning.

As part of the final exam in my Fall semester Microbiology course last semester, I asked my intrepid micronauts in Biology 350 the following question:

Please draw a cartoon related to course material or microbiological interests you have developed during this semester.

I was pleased with and amazed by the results.  May I share them with you?

Mariko is clearly wearing the "microbe-colored glasses" I have tried to impart to my students.  A new perspective!

Kailee was intrigued not only by EPEC, but by the Tir-Intimin system:  Type III secretion systems introducing a bacterial-specific receptor into the afflicted eukaryotic cell target!

Madison shares my fascination by the "Ron Swanson" character from the much missed television series "Parks and Recreation." Here Ron Swanson refuses to call Streptococcus by its true name, in order to establish and maintain dominance.  It's the Swanson Way.

Macaulie pleased me by internalizing one of the central lessons of my class:  avoiding "centric" thinking.  One of the "Deadly Centrisms" remains "colicentricity" where even fine microbiologists think all bacterial are just like E. coli.

I didn't have as much time as I would like to cover innate and adaptive immunity in my course, but Emma clearly was taken by the concept of cytokine storms as a pathogenic strategy.

Cheyenne had clearly thought deeply about the idea of "fingerprinting" people via the microbes on their skin.  I really like to closeup of the fingerprint!

As I mentioned above, my time was limited where innate and adaptive immunity were involved in my class.  But Reilly was fascinated by the way that M cells internalized, processed, and presented antigens to the rest of the immune system!

I have been a long term fanatic about symbiotic interactions.  Ruth shared my interest by depicting the fabulous relationship between Euprymna scolopes and Vibrio fischeri----and the quorum sensing necessary to create light!

Taylor has clearly paid close attention to my many Microbial Sermons.  She knows what you and I know:  it's a microbial world, and we just live in it.

Olivia was the official class "punster."  One of our lab exercises demonstrated natural transformation of antibiotic resistance genes in Acinetobacter.  Many students don't appreciate the prevalence and promiscuity of horizontal gene transfer in the microbial world. A delightfully bad pun was vintage Olivia.

Hailey was highly resistant (!) to my MicroTwitter assignment.  So I am not surprised that some Twitter H8r-ade made it into this assignment in an amusing way.

Emily shares my love of "low" humor and bad jokes.  So her depiction of microbial competition and niche exclusion is unsurprising, amusing, and illustrates a central point of microbial ecology well.

Olivia ("The Other Olivia" or "Olivia #2") has quite the creative mind.  Notice the diverse types of information from my course that appears in this illustration of "Enteric High School" (I can't wait for the musical)!

I see horizontal gene transfer, type III secretory systems, (-) strand RNA virus issues, square halophilic bacteria, the Entner-Dourdoroff pathway, and bacteriophages.  Microbial High School forever!

As an educator and High Priest of the One Microbial Truth (that is, there is only one microbiology course at my institution), I'm often worried what my students "take home" from my class.  It is clear that some of the ideas and concepts I presented now live deep within the brains of my successful micronauts from Fall 2015.  

What do your students remember from classes?  What makes them both smile, and recall important concepts?

Again, Happy 2016!

Thursday, December 24, 2015

Happy Luxmas 2015!

Well, as most people know, I am something of a #MicrobialSupremacist™.  That is just how I roll, microbially speaking.

So my holidays are required to revolve around microbiology.  And this is a good thing, not a "yuck" thing.

For example, I love teaching my micronauts that bacteria can make ice form.  Yes!  Pseudomonas syringae makes a protein on its surface called (rather uncreatively) the ice nucleation protein.  Ice nucleation protein, as its name suggests, catalyzes ice crystal formation in a chain reaction.  I have written about this before, with many informative references.

This video (from my Fall 2015 Microbiology course at the University of Puget Sound) shows supercooled deionized water. One drop of Pseudomonas syringae and...well, see for yourself.

This protein is used in snowmaking machines, by the way, and is commercially called Snowmax.  So yes:  you are skiing the microbial slopes, friends!

I also enjoy using reporter gene fusions in E. coli to create colorful displays.  I used GFP and RFP to draw this festive bit of Petri dish art.

Now, again, anyone who knows me understands I have a mania for bioluminescence.  So I naturally have created some Luxmas™ (lux for light production) displays on Petri dishes, using Photobacterium leignothi as "living paint."

Finally, my brilliant and artistic mathematician wife Dr. Jennifer J. Quinn (that's right:  I am married to "Dr. Quinn, Mathematics Woman") is SO tolerant of my microbiological mania.  She allowed me to put up a microbial Luxmas tree year round.  Here it is tonight.  It is festooned with a blazing Shewanella from the Mudwatt people, has various GiantMicrobes on it, and features beautiful Petri dish ornaments from the fabulous artist Michele Banks.

And here is my Luxmas Tree with bioluminescent ornaments.

Finally, Dr. Quinn helped me to create this wonderful time-lapse video a few years ago.  I adore it.

Thus, I wish each and every one of you a wonderful Luxmas, with much microbiological merriment.  I salute you and your microbiota!

Wednesday, December 23, 2015

Microbiology and Creative Extra Credit

Once again, the semester has gotten away from me!  I have many things to post over Winter Break about the past frantic yet rewarding semester, but let me start with this tradition of mine.

During the past few years, I have been encouraging students in my freshman level "Introduction to Cell and Molecular Biology" and junior/senior level "Microbial Diversity" courses to explore course material via creative approaches.  I have posted about these efforts in previous blog posts, such as this or this.  

I do this via an extra credit "creative" assignment.  I scaffold it as follows:  (i) the student must get verbal approval from me about their idea, (ii) the student must turn in a one page description of their project for review, and (iii) turn in their project!  The scaffolding serves several purposes.  First, I am able to ensure that the idea sortofkindof matches course material. Often I discuss the approaches and directions of the proposed project.  More importantly, I am able to work with the student to make sure that the proposed project doesn't eat into their study time (I don't know about you, but when I was a student, I would do nearly anything but study as finals approached:  clean my room, write fiction, fight with loved ones...).

This year's microbiology class has produced some interesting creative approaches to the field I would like to share with you, ranging from the very serious to the whimsical.  I'm proud of my micronauts, as usual.

First, Macaulie decided to make microbially themed cupcakes, as can be seen here.

Strangely, the STD ones were the last to be chosen.  Hmmm.  At the same time, I was pleased to see basic course concepts reinforced multiple times.  And tastily, too.

One of the things I ask my micronauts to think about is how microbes are portrayed in the media---versus the MicrobialTruth I preach in my class.  This led Cheyenne and Taylor to create these microbially relevant magazine covers.

I did spend quite a bit of time chatting about antibiotic resistance, so this makes sense.

I take no responsibility for the beer references, but we did a lab exercise with lactic acid bacteria.

Well, of course.

I guess that the lab exercise isolating Sporosarcina from areas that dogs, well, watered has stuck with them.

Brian has had some interesting results in lab brushing his beard onto Petri plates with various media this semester.  Here is just one example.

Um. Microbial diversity reigns.

So his "beard-ome" artwork was expected...and fabulous.

Mariko loves Disney movies, and decided to share a "Whole New (Microbial) World" with the class.

A student from my class who does not wish to be named created something quite lovely here---a different view of microbial bullying and antibiotic resistance.  I was VERY impressed with the approach, creativity, and sentiment!  The student should be very proud.

One of my favorite historical figures from microbial genetics is Jacques Monod.  He famously once opined that "What is true for E. coli is true for elephants," making clear the centrality of biology. So Kailee created this is honor of that MicrobialTruism™.

One of the things that has long bothered me about MattersMicrobial is the constant drumbeat of negative PR in the popular (and sometimes scientific) press.  There are so many #SwabStories where folks swab a particular area and find it---surprise, surprise---covered in microbes.  It's a microbial world, and my micronauts and I just shake our heads at the headlines and false-scary pronouncements. Here are two video approaches to that problem.

First, Hailey became a #MicrobialMythBuster.
Next, Reilly and Madison created #ClubMicro.

Best way to keep microbes away from clubs?  No people!

Olivia created a story based on "Cinderella" that she called "Bacterella."  Here are some images from her informative and amusing creative project.

What is interesting here, again, is how many concepts from class appear in this microbiologically themed fairy tale.  There are many ways to learn, indeed.

Emily and Emma had a plan for this particular assignment. But they would not tell me the nature of their plan, assuring me that I would "like it very much."  I told them that they still needed to hand in their one page summary of the project.  So they did.

Um.  I didn't ask if they had relatives in the NSA.  Seems likely.

Anyway, what Emily and Emma brought was interesting.  Each person in class got a Petri dish.  There were several choices.  Here was mine.

Inside the Petri dish was a booklet.

The booklet had good information.

Did I mention the stickers?

So I did indeed like it very much.  Don't you?

Last, but certainly not least, was a fun video by Olivia and Ruth, about bacterial bioluminescence and lovely, lovely quorum sensing. Notice the symbiotic aspect!

Some folks deride these kinds of projects.  I don't.  The reason? Again, there are many ways to learn.  We honor diversity in education; why not diversity in approaches to learning?  This is but another arrow in the quiver of our pedagogical strategies, I think.

I have found that people learn best when they have "ownership" in the process.  And having a carefully chosen "extra credit" creative project can genuinely reinforce concepts from a course in a way that will be long lasting and memorable (instead of filling in a blank on an exam).

I am proud of the efforts of my micronauts, and I hope you are as well.

Saturday, October 31, 2015

Time for a #MicrobialHalloween and a #ParasiticHalloween

Now, anyone who knows me knows that I simply adore Hallowe'en. I always have.

Yes, I spread bioluminescent bacteria on Petri dishes, and then inserted them into a pumpkin.  A #MicrobialJackOLantern.
So it should not be a surprise that I like to incorporate this special holiday into my classes, and have a long history of doing so. Today, Saturday, is Hallowe'en.  But even so, my Microbiology students on Thursday, and my Symbiosis and Parasitism freshmen writing students on Friday, participated.  I would like to share their creativity and humor with you.  Learning can take many forms, I have found.  Plus it is fun!

First, one of my #Bio350 students shared their own #MicrobialJackOLantern with me.

Nothing wrong with some streptococcus and a microscope on a rainy Hallowe'en.  Am I right?  Here are some close ups.  I think that these were made by Brian in my class.

First, a Streptococcus-O-Lantern:

Then, a MicroscopicPOV-O-Lantern:

And another student in my #Bio350 course,  Ruth,  just made an interesting pumpkin---a #BacteriophagePumpkin?  A #PhageOLantern?

Now, I generally don't dress up for Hallowe'en any more.  This year was an exception, as you will see a bit later.  But I encouraged my #Bio350 micronauts to let their OMG™ (overwhelming microbial greatness) show itself this holiday.  And some of them did precisely that!

Here are some of my micronauts in #MicrobiallyThemed costumes.

Then, a video.

Let's view what we are seeing here.  

Madison would love to be a "genomic islander."

Kailee and I agree that calling a tool for spreading microbes on a Petri dish a "hockey stick" does a disservice to the sport.  So she expressed that well, and in competitive spirit.

Olivia decided to show her bacterial side in her outfit.  Yes, the blue flagella say it all.

Here is a close up.  I adore seeing transcription and translation taking place as a creative exercise!

Macauley decided for a more minmalist approach, depicting Serratia's lovely prodigiosin, and inexplicably carrying sriracha sauce.  The color?  Maybe the antimicrobial effects?

Hailey tried out a "Two Face" approach to microbiology, as you can see.  She even burned herself with a hot glue gun to promote her craft.

Brian honored his commitment to sterile procedure by depicting that goal via costume.  I don't know about the white hair.

Emily and Emma were inspired by a recent discussion of riboswitches in class, and became "ribos-Witches."  Very creative!

Finally, Cheyenne and Taylor created a two part costume showing the medieval view of plague, and a plague victim.  The makeup was impressive.  And fits in, I think, with some of our zombie interests in popular media these days.

Very nice!  But what about me?

Another one of my obsessions these days is the small but mighty tardigrade.  My long suffering wife Jennifer Quinn has allowed me this obsession, as she does with my microbial tattoos.  After all, they are much cheaper than red sports cars.

I have enjoyed watching them under the microscope.

Unsurprisingly, I tend to collect tardigrade toys of the plush variety.

And even of the 3D variety.

My wife in fact built me a tardigrade table for my birthday this year.

And even commissioned the great Brian Mock to create a tardigrade sculpture for me.

Yes, I seem to have a problem.

So it should not be a surprise that when I decided to dress up for Hallowe'en for my classes, I would choose a tardigrade...and its associated microbiota.  Here is an explainer.

And a close up of the truly fabulous mask Jennifer Quinn made for me.

I also received a nice surprise from one of my #Bio350 micronauts on Friday:  my very own #MicrobialJackOLantern with artwork of the logo for this year's microbiology course.  

As you can guess, I was very touched by this particular #MicrobialHalloween!

My other course this Fall is my freshman writing seminar revolving around symbiosis and parasitism.  So a #ParasiticHalloween sounds grand.  Several of my students dressed up (and I did, too, as my Disco Tardigrade).

In class on Friday, we watched "The Host," an old episode from "The X-Files," about a mutant giant fluke parasite (very appropriate given the course topic).  I also brought gummi worms for the full effect.


Theo is quite interested in parasites in the fossil record, so I shouldn't be surprised at his costume.

Cotton, on the other hand, has an deep fascination with sharks. This appears to be a "cookie cutter shark."

Carmen and Genevieve had a costume that, while not related to symbiotic associations, represents one of my favorite movies.  Can you guess what it is?

Braith did a pretty awesome job depicting a banana slug.

And I have to admit, Mary had perhaps the most horrifying costume of all.

Get it?  Sigh.  This one is less pointed than in earlier years, at least.

But when it comes to humor, I think that JT and Lauren got the greatest laughs with a highly appropriate costume that cost next to nothing.  Such creativity!  Here is the video.

You see, they are depicting the Schistosomiasis parasite, seen here.  The larger male has a channel in which the female attaches.

You can read more about these seemingly "loyal" parasites, and the serious diseases they cause, here.

So in all, it was QUITE the Hallowe'en.  I hope yours was as frightening fun as my own!