Sunday, December 30, 2012

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.    

Friday, December 21, 2012

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!

Wednesday, December 12, 2012

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!  

Sunday, November 25, 2012

Microbiology, Art, and Pedagogy!

In this season, we all have much about which to be thankful (other than, for our non-vegan colleagues, the turkey):  family, friends, and health.  I am also extremely thankful, unsurprisingly, to be a microbial geneticist in an era when such wonderful (well, as the young folks say, deeply awesome) new information seems to appear daily!

When it comes to matters microbiological, one of my favorite stops on the internet is Elio Schaechter's (and his fine co-bloggers) microbiologically-themed blog, "Small Things Considered."  This blog has provided me with a great deal of fascinating, up to date, and insightful information that not only amazes my microbiology students, but delights me as well!  I honestly feel that the "blog" approach to scientific papers can be very helpful to students pedagogically as they learn to read and analyze journal articles:    distilling down complex papers to inclusive concepts, giving background to the "inside baseball" aspects of cutting edge research, and so on.  Students agree it helps a great deal, particularly when they need to summarize and present papers, and I have ample evidence to back that assertion up.  Several other people use a similar approach to cutting edge science as well, of course, including but not limited to Carl Zimmer, Ed Yong, and Laurence Moran.  

However, Elio's blog is the place to go for Ongoing/Overwhelming Microbial Goodness™ (my version of the internet acronym "OMG").  Run, don't walk---electronically speaking.

Recently, Elio wrote a short essay at "Small Things Considered" celebrating art in microbiology, with many interesting and useful links.  This is a particular interest of mine, and I thought I would comment a bit further on the topic.  Elio is correct that there is a venerable tradition (perhaps started by Fleming himself, as is related in the blog post) of microbiology and art.  The art can be whimsical (as with the "boxing bacteriophages" created by Fleming and reproduced in the blog post).  It can be serious, as in the intricate and scientifically accurate art of David Goodsell.  Here is a sample to illustrate what I mean:

The above would be Dr. Goodsell's interpretation of E. coli from a molecular point of view---based on what we know about the "machineries of life," which is also the name of a wonderful book by Dr. Goodsell.  The description of the illustration above is here.

There are also artists who straddle the divide between the accurate and whimsical, and do it very well indeed.  Michele Banks, as "artologica," does exactly that.  Her many interesting artistic interpretations of biological concepts---including, famously, microbiology, can be seen at her Etsy shop.  In fact, I once asked Michele to create a bit of artwork depicting predatory microbes, a subject I try to study with undergraduates in my laboratory.  She asked for references about predatory microbes,  and I sent them along.  Her creation impressed me quite a bit, as it depicted many concepts from the articles I sent Michele.  A nice blend of the artistic and the microbiological!

The places that artists can go with this topic are are a wonderful intersection between microbiological facts and artistic creativity.  For example, here is E. coli created as a glass sculpture (link to the website describing the artwork here):

I can even go to a very odd place in this "sculpture business."  Kombucha is a naturally occurring biofilm composed of yeasts and bacteria that ferment the drink of the same name from sugared tea. A Washington state artist, Nole Giulini, actually uses these biofilms to create sculptures, which she calls "Boschlings."  Here is one, to give you some idea of the quirkily artistic results:

Ms. Giulini goes further and even has a YouTube video illustrating how to create and use the biofilm as a medium for her sculpture, complete with background music!  What a remarkable intersection of art and microbiology, don't you think (even though the video description below describes kombucha as a fungus, when it is, again, a biofilm composed of various species of yeasts and several genera of bacteria, usually including Acetobacter xylinum)?  Here is the link to the video, just in case my skills at embedding video are, um, underdeveloped.

In the last few months, another "microbiological art" approach has been described in the media.  It is almost an analogue of photography, using UV radiation and the pigment producing bacterium Serratia marcescens.  Zachary Copfer's interesting approach is described here.  Below is an example of his approach, from that article:

So, as with Elio's blog entry, and the many links that can be found there and online, it is clear that it is possible to create art using microbiological topics or even microbiological material.  Certainly, I have done my share with bioluminescent bacteria, as I have written earlier on this blog (including "portraits" painted with luminous bacteria, as Elio showed using an illustration my wife made of yours truly).  Heck, my wife and I even put together a Microbial Xmas Tree last year, making "ornaments" from nutrient Petri plates, and drawing "stars" on them with luminous bacteria:

My involvement with microbiology and art began in an interesting fashion. Several years ago, I was asked to teach an "extra" lab section of Genetics at the University of Puget Sound (it was a huge class, and needed more lab sections taught than usual).  In that class, I met a young woman who told me that she was interested in the intersection between art and microbiology---because some microbes, she knew, made pigments.  True enough!

I had recently seen an interesting 2010 journal article by Charkoudian and her colleagues, describing how to use various species of Streptomyces as a source of pigment for student "art projects."  It is a wonderful paper, describing using the "artistic" aspects of the pigment as a "hook" for teaching about microbial biosynthesis, chemical properties of pigments, the nature of paint, and some discussion of artistic principles, even when one of the sample products is not precisely "classical" (from the journal article). Viva, Streptomyces?

I was not able to obtain the "microbial palette" that actinobacteria can provide according to that journal article.  But I did know that some of my "in stock" microbes produced interesting pigments:  Chromobacterium violacein produces the purple pigment violacein, Serratia marcescens produces the red pigment prodigiosin (shown above and used by Zachary Copfer to make "Serratia photographs"), and Micrococcus luteus produces yellow carotenoid pigments.  

The student in question, Kayla, was very excited by the possibilities.  In collaboration with an organic chemist at the University of Puget Sound, the inimitable William Dasher, Kayla began to isolate pigments and begin to experiment with them in pigments (focusing on alcohol-soluble pigments for ease of work).  As you can see, the results were lovely.

Kayla's best results were with violacein and prodigiosin, and she began to experiment with adding them to her paints.  Soon she created some lovely print-panels of art---using microbes as their source and subject!

She finished by creating a triptych of artwork that stands to this day across from our departmental office (complete with an explanatory label)---and it is a source of continuing interest by visitors, and pride from students and professors alike.  This is one of the goals of a small liberal arts institution:  to mix science and the arts!

I have also had two wonderful "microbiology and art" experiences in my own classroom.  These events demonstrate how art can extend and assist with pedagogy---especially for more "visual" students.  It's not just about art:  it can also be about learning---despite what a student might think while preparing for an exam!

Two years ago, I was doing what I could to keep my microbiology students (my "micronauts") engaged and attentive.  So it is true I sometimes become a bit flamboyant as I lecture.  I stood in front of one young woman in that class, Sarah, and told her that even as I spoke, I was emitting "Doc Martin associated microbes," just as she was doing the same thing with her own unique microbes---that there were clouds of microbes surrounding us at all times.  I wondered aloud what was happening at the intersection of the two "clouds."  Needless to say the grotesque (to the students) aspect of this discussion held their attention---and the topic of human emitted aerosols of microbes has in fact become of interest to scientists here and here.

But imagine my surprise, a year later, when Sarah (pictured next to her artwork) sent me the following piece of art (with apologies to Charles Schultz and the infamous "Pigpen").

Sarah is in dental school now, and is mindful of Microbial Supremacy, it is clear!  I know that she will bring what she has learned (and is learning, now) to her practice as an excellent dentist.  Especially when she considers how dental equipment "aerosolizes" microbes in the human mouth, as reported here.  Gulp!

Last year, in my microbiology course here at the University of Puget Sound (and it is my only chance to preach the Microbial Gospel to students at my institution), I worked hard to find different ways to "reach" students who hadn't had much exposure to microbiology (forgive the pun, please).  I created an extra credit "creative" assignment.  I asked students to record short "video logs" describing what they found most interesting about microbiology.  One student, Alena, said she was uncomfortable with such a project.  Could she create a piece of artwork instead?

I thought it over, and suggested that Alena create a bit of art that depicted a biofilm, show that biofilms are composed of many species of microbes in nature, that antibiotics don't work well on biofilms, that bacteriophages can in fact attack biofilms, how biofilms disperse, and the role of quorum sensing in the formation and maintenance of biofilms.  If you need to know more about biofilms (a topic which I think should be in the freshman curriculum, along with many other microbiologically-relevant topics) start here and then watch this.  

In any event, Alena accepted the challenge.  Imagine my surprise when a week later, Alena presented me with the following (to the right of her photograph below):

What was most interesting to me was seeing how well she understood the process of biofilm formation (when I asked about it on their final exam)---because of her visual learning during the process of creating her cartoon art!  This suggests that "artistic approaches" can be of genuine pedagogical value to many students.

Alena just returned from helping the Red Cross deal with Hurricane Sandy.  I'm very proud of her, and think she will become a caring and superb physician.

It is increasingly clear to me that art and science can mix in ways that are of distinct advantage to both participants:  new and interesting artforms can be created, and science can benefit from the visual in many ways (and at many levels).  So the idea of "drawing" a fun cartoon on a Petri dish can in fact be used to illustrate important concepts in microbiology---and perhaps just as importantly, help students learn in nontraditional ways.

I wonder what will be next at this intersection of microbiology and art?


Monday, November 12, 2012

Honoring Those "Microbial Vests"!

I fully admit it:  I am obsessive about microbial supremacy.  After all, that is sort of my laboratory motto:

Anyway, for years I have been buying scarves and neckties from the great people at "Infectious Awareables."  At several American Society for Microbiology meetings over the years, I have been able to speak to Dr. Roger Freeman and his lovely wife Felice Freeman (the owners of Infectious Awareables) several times.  I would buy microbially themed neckties and have my students sign them with marking pens as souvenirs of their taking my class...and then there were those microbially themed vests!

Both of the Freemans always loved the microbial vests that my mother made for me over the years, using their scarves as material.  They were saddened when my mother passed away in October of this year, after her long and courageous battle with ovarian cancer.

So I was touched when Dr. Freeman asked to write a few words about my mother and those vests of hers to be published in their newsletter here.

My mother was "psychologically Amish," and was uncomfortable with praise.  But her vests---and her life---merit that praise.  Rest well, Mom.  You fought a tough battle, and now can rest.

I will tell your story to anyone who sees one of your vests.  And so will Dr. Freeman, I'll bet!  My family and I are very grateful for your kind words.

Sunday, November 4, 2012

A Microbial Hallowe'en!

As October had not been the most upbeat month for me, personally, I was truly looking forward to my favorite holiday:  Hallowe'en.  Even better, it fell on Wednesday of last week, a lecture day for my Microbiology class!  So I began to plan...

People who know me well are very much aware of how much I adore Hallowe'en, as well as (of course) microbiology, being a proselytizing microbial supremacist and all.  Thus, it is no surprise that I have often tried to mix my two favorite topics.  Last year, my lovely and talented wife Jennifer Quinn carved me a "microscope" pumpkin to good effect.  When I say that I "married up," you now can see why.  But just wait.

I even tinkered a bit with my camera, and Photobacterium leiognathi (a very bright strain called KNH1, isolated from Kane'ohe Bay in O'ahu, Hawai'i, by the great Ned Ruby and then-student Eric Stabb) to create this, um, unusual self-portrait last Hallowe'en...

I carved Petri dish sized holes in the pumpkin, spread some Photobacterium leiognathi on supplemented nutrient medium, incubated the plates, inserted them into the pumpkin, took a timed exposure in my darkened kitchen at home, and voilá!

Thus, I wanted to make this year's Hallowe'en a bit special for many reasons, and also wanted it to involve microbiology.  Mission accomplished, as you shall see.  

First, I offered my long-suffering Microbiology students extra credit if they actually dressed in some microbiologically relevant fashion in class on Hallowe'en.  These students are generally seniors, and haven't had any real exposure to the subject before my I was curious where this would take them. Let's have a look, shall we?

I appreciated the first student entry, who made his "identity" clear by both the color of his hoodie and helpful labels.  Yersinia pestis is an interesting organism, it is true!

This student wore a "double duty" costume.  She informed me that she was green fluorescence protein (GFP).  At first I was a bit dubious of her choice, as GFP originated with a eukaryote...but I have certainly discussed GFP in class as part of gene fusion technology that helps us to understand gene regulation in bacteria.  Double duty?  It turns out her Biochemistry course also had a class meeting on Wednesday and the professor had asked the students to appear in relevant costume.  The infamous two-costume problem...solved!

Other students were more interested in the intricate "mechanisms" behind microbes (and they are remarkable nanomachines, it increasingly appears).  Here a student has constructed and was wearing a model of the prokaryotic flagellum! At least it wasn't motorized, which could have been hazardous to nearby students, PMF or not!

Here we have a student who became quite interested in the fascinating and vital cyanobacteria, and thus dressed the part, complete with nitrogen fixing heterocyst.

Earlier in the course, I spent some time discussing cellular size and microbes, since newcomers to microbiology assume that all microbes are...small. Not so!  One of the "giant microbes" we discussed was Thiomargarita, which is composed of a thin layer of cytoplasm over a huge nitrate filled vacuole (kind of "cheating" when it comes to the size issue, when you think about it).  Giant, filled with glittering bling-like sulfur granules, carrying its own terminal electron acceptor like a SCUBA tank, and being named in way reminscent of a refreshing adult beverage...what's not to love?  So the FOUR students above presented their own unique interpretations of Thiomargarita.  I was impressed!

Archaea can have attitude, as well as a central role in our biosphere.  I try very hard to impress upon students the ubiquity and importance of this Domain of life.  At least this student, dressed as Pyrococcus furiosus (discovered by the inimitable Karl Stetter) was representin' that attitude of global relevance and control!  

Then there were students who opted to dress as a microbiologist, rather than a microbe.  It was interesting to learn which microbiologist sparked their creative sides, costume-wise.  Here a student decided to dress up like one of my Microbial Heroes™, Carl Woese.   It's a decent likeness, as you can see (the student is on the left).

On the other hand, one of my other students went more formal, trying to "be" another Microbial Hero™ of mine, C.B. van Niel. I think he did pretty well.  

Here is a meeting I would have loved to have witnessed:  Carl Woese AND C.B. van Niel!  What did they talk about?  Or did they ever actually meet?

In addition, being Hallowe'en, three students brought cookies to class!  I didn't ask them to do so; they did it on their own (and I very much was touched by their love of matters microbial!).  The cookies on the right were student designed and beyond impressive (also tasty), but the cookies in the middle and on the left were inspired by this recipe, which is filled to the ever-loving meniscus by sheer microbiological awesomeness!

Then it was my turn, to bring some microbiological something-something to Hallowe'en in class on that special day.  And I was able to do so, courtesy of my artistic wife Jennifer Quinn, as I alluded above.  What we did was to look up various microbiologists, and then have Jenny "paint" their portraits onto appropriate nutrient agar plates. Incubate and then take a nice long exposure...and I think what we did was fun, and a bit artistic?  And it was fun to work with my wife on a project!

First, Jenny---being a mathematician (and sharing a birthday and Pi Day with the gentleman)---tried things out with Albert Einstein.  It worked out pretty well, I think.  The story of that particular photograph of the great man is to be found here.

Then, of course, it was time to try out some Microbial Heroes™ of mine, from history and our current period.  The above was an attempt at the great Louis Pasteur.  The problem was that the plate slid a bit during the "painting."  But that's okay:  it has a "Zombie Pasteur" vibe that I actually like (and Jenny did spend some time "painting" Edgar Allen Poe portraits using luminous bacteria with great and spooky success!).

Carl Woese is one of the names I need all of my students to remember. He is the architect of the great Tree of Life, and "discoverer" of the Domain Archaea.  Historically, he never gave up, and fought a scientific "good fight" until the paradigm shifted in his favor (as in the Microbe World video linked above).  So why not put his names up in light, to honor him, so to speak?  It's actually not easy to paint on these Petri dishes, since the bacterial culture doesn't have color to it (different from the solid medium).  Still, I think it is a decent likeness!

Another Microbial Hero™ of mine is the late Lynn Margulis.  Opinionated, fearless, and indefatigable, this dynamic scientist pushed the paradigm shift that chloroplast and mitochondria were once bacteria, even before molecular 16s rRNA data became available---now respected and taught as the endosymbiotic theory of cellular evolution.  I once spoke with her on the telephone (about predatory microbes) and told her that I felt that cyanobacteria and bacteria had been cruelly enslaved by primitive eukaryotes billions of years ago.  "Now you've got it," she exclaimed in reply.  To be sure, she was complex, but unforgettable

One of the things I most enjoy about microbiology is that even famous microbiologists will speak with enthusiasm to folks like myself, who are more educators than bench scientists.  Thus, I have gotten to know the very impressive Jo Handelsman over the years.  Jo coined the term "metagenomics," the method of studying all of the DNA in an environmental sample, regardless of its origin.  She is tireless in her championing (by example) of mentorship and advancing education in microbiology (and in general), especially for women and underrepresented groups.  She brings out the best in people, and by example.  I hope she likes this portrait! 

Over twenty five years ago, when I decided to leave the biotech industry (actually, I didn't "decide;" I had been laid off), and wanted to return to academia and the teaching of undergraduates, I needed a new research system to introduce to those undergraduate students.  Thus I returned to Bdellovibrio, first introduced to me as a sophomore by the late Syd Rittenberg at UCLA.  A former student of Syd's, Ned Ruby, worked a bit with Bdellovibrio. He was moving away from that system, and into a fascinating symbiosis between bioluminescent Vibrio fischeri and the Hawai'ian Bobtail Squid, Euprymna scolopes.  Ned brought me up to speed on working with the often-cantankerous and recalcitrant Bdellovibrio, and thus I made a new friend and colleague.

Over the years, Ned Ruby and his long time partner, Margaret McFall-Ngai, have carefully dissected their wonderful squid-vibrio symbiotic system to great acclaim.  Ned works with the bacterial part of the mutualistic association, while Margaret works with the eukaryotic side.  Both of them have learned a great deal about both sides of the scientific equation---and science has greatly benefitted as a result.  Just as the squid and vibrio are interactive, so are the scientists involved!  Ned's deep understanding of bacterial genetics is a valuable resource to many, and Margaret's "conversion" to microbial supremacy (more accurately, the vital role that microbes play in animals and plants) has been an inspiration to me.

My wife and I have thus known Ned and Margaret for many years, so a portrait of them seemed like a great idea.  I hope they like it!

Finally, my wife created a special "surprise" for me---I certainly didn't ask her to create this last bit of "art."  She took a photograph that was taken of me while we were in New Zealand last Spring (at the hot springs of Rotorua), and turned it into a bioluminescent portrait of me.  

Perhaps this last is the "trick" of the microbial "trick or treat" I brought to class that day!

In all, a wonderful and enjoyable (and microbial) Hallowe'en!  Onward and upwards!