Sunday, August 30, 2015

"Never Really Alone" with Rob Dunn

The summer is sprinting away, leaving me behind!  Tomorrow, the 31st of August, is the first day of classes for Fall 2015 at the University of Puget Sound.

Whew!

This semester, as I have been discussing in prior posts, I will be teaching Microbiology to 16 hopefully avid "Micronauts" (juniors and seniors).  In addition, I will be teaching a freshman writing course revolving around ideas in symbiosis and parasitism, which I call "Never Really Alone."  Here is the course description.


Last Fall---the first time I taught SSI-165A---we had quite a wonderful class, and were fortunate to have a number of leading experts in the study of symbioses and parasitism "televisit" my classroom.  My previous posts are a testament of the willingness of some awfully famous folk to do "outreach" to my freshmen, and I am quite grateful.

The last of our speakers last Fall was Dr. Rob Dunn of North Carolina State University.  Rob's willingness to chat with my class was a particularly big deal to me, since he is the author of one of the books I use in my course, the compulsively readable "The Wild Life of Our Bodies:  Predators, Parasites, and Partners That Shape Who We Are Today," which is wonderful proof of what I try to teach my freshman:  that we are all walking ecologies!

Rob Dunn studies a dizzying array of systems, and has brought together quite a group of researchers to investigate them, as a look at his  blog website and laboratory website amply demonstrate:  belly button microbes, ants in unusual places, tracking housecats, life in the dust of our homes, microbial components in beer, heartbeats...and the small mites that live on our faces.  

Biodiversity everywhere!

One of the things that Dr. Dunn and his coworkers have studied recently are those fascinating and odd Demodex face mites that we all have.


As you might expect, this topic gained a lot of interest.  Not only did the Dunn lab find that we all carry these tiny passengers on our very faces, but that there is more than one species resident!


Ed Yong wrote a wonderful summary of some of the work that Rob Dunn and coworkers have carried out.  We are truly never alone!

As in previous "televisits," I had my freshmen students read some of the work of Rob Dunn, and come up with questions that I sent to him. Then, Dr. Dunn visited our class via "Google Hangouts" and discussed those questions with my class.  The students, and yours truly, were very, very lucky.  Here is that visit.


It is no secret that I adore having students explore science using nontraditional, even artistic, approaches.  One young woman in our class made some plastic models of Demodex, as you can see below.


One of the questions that seemed to interest/concern my students about Demodex is how they spread from person to person.  At one point, Dr. Dunn suggested that they might fly through the air like dust motes.  This inspired the young woman in class to try to represent a paratrooping Demodex!


It was a truly memorable session, and a wonderful speaker and topic to finish up that series.  As before, my students created a "thank you" poster for Dr. Dunn.


And the artistic friend of one of our students created a sketch of Rob Dunn to commemorate the visit.


So in all, I really enjoyed teaching "Never Really Alone," and the "televisiting" speakers remain a big reason.  The students agreed.  I hope that, if nothing else, I gave them an appreciate of the "wild life" that make each of them into walking ecologies!


Many, many thanks to Rob Dunn and the other visiting speakers: Jack Gilbert, Ed Yong, Margaret McFall-Ngai, and Seth Bordenstein. 

Tomorrow, I begin teaching the course again to a new crop of freshmen---I wonder whom I will be able to coax into televisiting to bring new ideas to these wonderful freshmen?  And to increase my own sense of wonder as well, of course.

Teaching science is a very, very satisfying profession with classes like my own.

Onward to the new semester!

Wednesday, August 26, 2015

"Never Really Alone" with Seth Bordenstein (Including Current News)!

Wow!  The new semester is coming upon us!  

As I have mentioned in earlier posts, I will be teaching my beloved microbiology to 16 micronauts (juniors and seniors) this Fall, as well as a freshman writing class (to 17 students).  This latter class revolves around the concepts of symbioses and parasitism throughout nature.  Here is the course description.

I was extremely lucky, last Fall, to have some truly remarkable people "video visit" my freshman class, as my prior posts demonstrate.  These visitors answered student questions and discussed their research and interests.  The students seemed to like it.  I know I did!

I was very happy to have the ubiquitous Dr. Seth Bordenstein of Vanderbilt University chat with my class last Fall.  At that time, he discussed how the "holobiont/hologenome" idea meshed with central concepts in symbiotic associations

Here is Seth's "virtual meeting" with last Fall's class!



What is particularly exciting as I write this post is that Seth Bordenstein and his coauthor Kevin Theis have JUST come out with a fascinating and critical "position paper" on this entire topic.  Here is "Host Biology in Light of the Microbiome:  Ten Principles of Holobionts and Hologenomes," as well as a press release from Vanderbilt on the paper.


Wonderful things to discuss with both of my classes this semester, truly.  Paradigms are shifting, readers.  Change can be evolutionary or revolutionary; the former is slow and the latter bloody.  Time will tell.  But as microbiology races on, it continues to change the way we look at most of biology.  Seth Bordenstein's work only underscores this MicrobialTruth™.

Here is the "thank you" poster that my class created from Dr. Bordenstein.



Here is the portrait that a friend of one of my freshmen last Fall drew of Dr. Bordenstein.



And this summer, Dr. Bordenstein came to visit my little undergraduate lab.  We had a great time chatting about symbioses, drawing "art" with luminous bacteria, and listening to music.



Thanks again, Seth, and I look forward to preaching the Holy Holobiont as a concept in my classes.  "Out of many, one," indeed!


And we are never truly alone, as the title of my class states, after all!

Monday, August 17, 2015

"Never Really Alone" with Margaret McFall-Ngai!

As the new semester implacably looms (about two weeks now!), I am remembering last year at this time.  What worked in the following semester.  What could be improved upon. My classes are always a work in progress, and a collaboration with my students. My brain is in quite a ferment (sorry about that) to make things better for the students.

As I have written previously, in the Fall semester last year, I taught my beloved microbiology to juniors and seniors here at the University of Puget Sound.  But I also taught a "freshman writing seminar" to students who had just arrived in Tacoma.

This latter course, which I call "Never Really Alone:  Symbioses and Parasitism Around and Within Us," is intended to introduce new students to critical reading, discussion, writing, and presentations.  Here is the course description.


I focused my course as I did in hopes of stirring up student interest, and teaching basic university skills. And I believe I did both!

One of the reasons for the student interest, I believe, was my luck in getting some very famous and fascinating people to "virtually appear" to my class and interact with my students.  I have been trying to showcase those experiences from last year, to see who I could induce to speak to my class in the coming semester.

Last Fall, I was honored to have Dr. Margaret McFall-Ngai as a participant in my class.  I have known Margaret for many years, and she is a world authority on symbioses.  This paper in particular is extremely important, along with this blog summary.  I had students read some of Margaret's work (including those two sources), and then submit questions to her before the "virtual visit."

So here is Margaret's "virtual visit" to last year's class.  Margaret was most comfortable with Skype (and I am not), so my recording of the session was not as smooth as it might have been.  Still, it was a wonderful opportunity for my students, and meant a lot to me personally.



As before, here is the "thank you" my students created.



And here is the drawing a friend of a student in my class created.


Thank you, Margaret!

Sunday, August 2, 2015

Honoring the Memory of Another "Microbial Hero": the Late, Great Ed Leadbetter.

The poet Rilke wrote that "Death is large" and it remains a sad truism.  One seldom notices the impact of a person until they are no longer present.  As I grow older, like most of us, I have begun to lose people who are important to me.  If the poem "Calmly We Walk Through This April's Day" by Delmore Schwartz states "Time is the fire in which we burn," it also points out that "Time is the library in which we learn."

To that end, let me honor the memory of the unforgettable microbiologist and mentor Dr. Edward Leadbetter. There is little point in my writing a short biography of Ed.  His son, Jared Leadbetter (also a microbiologist!), wrote a wonderful and moving memory of his father at the link above.

Today, in Woods Hole, Ed's friends and family are remembering his life with laughter and appreciation.

My connection with Ed is not that of a son, a graduate student, or a postdoctoral scholar.  When I left the biotech industry and tried to return to academia, I knew that I loved microbiology.  In particular, I adored "unusual" or "undomesticated" microbes.  I always have, even from the time I was a boy and first streaked out a plate of bioluminescent bacteria.  So as a new tenure track assistant professor at Occidental College in Los Angeles in 1995, I looked for ways to capitalize on my abundant enthusiasm for Matters Microbial™.

I read about the Microbial Diversity summer course, held at the Marine Biological Laboratories in Woods Hole, Massachusetts (notice the current co-director of the course, by the way!).  As an older applicant, I didn't think I had much of a chance of being accepted. Apply I did (because if I did not apply, I was assured of not being accepted!).  Wonder of wonders, I was accepted.

The Microbial Diversity course changed my life as an academic. I wish I could put those words in letters of microbial fire (similar to what William Blake claimed to see as he made his engravings). What I learned and saw in that course is part of my daily life in the lab.  

My family would argue it is part of my daily life in general, I suspect.

The late Abigail Salyers was one of my instructors for that life-changing course.  Ed Leadbetter was the other.  Here was my Microbial Diversity course group photograph in 1996 (I am second from the right in the back row, while Ed is fourth from the right).

As I have mentioned in my earlier blog post, Abigail was very influential in my life. So was Ed. Ed lacked the, um, flamboyance of Abigail the investigator of colon-inhabitating microbes---but Ed knew seemingly everything about microbes.  That love of microbial diversity really struck a chord with me.  Ed's focus and philosophy turned out not to be surprising; he had taken the first incarnation of the Microbial Diversity course from C.B. van Niel himself.  You see,  C.B. van Niel is the "father" of microbial diversity.

I honestly felt that the American Society of Microbiology ought to have followed Ed Leadbetter around with a microphone and recording equipment and just let him talk.  I cannot think of a single exchange with Ed where I did not learn something new and interesting about microbiology.  He would just matter of factly tell me things that I had never heard or read before.

For example, I had a protocol for measuring the amount of tryptophan in a sample by using a cell free supernatant of a culture of Chromobacterium violaeum.  The Chromobacterium makes enzymes that convert colorless tryptophan into purple violacein, easily detected spectrophotometrically.  Wonderful student project, right?  Except I had trouble getting it to work in student hands. When I asked Ed about it, he calmly agreed and told me that "lab strains" of Chromobacterium appeared to lose the ability to have active enzymes in their supernatant!  He reminded me again that "domesticating" microbes often led to changes in phenotype, just as Beijerinck and others had reported in the early days of microbiology!  This idea has seldom been far from my thinking about microbiology; Ed often told our class that microbes were living things, not reagents, and had their own evolutionary agenda.

As with most Matters Microbial™, the years have only shown that Ed Leadbetter was right.  If Barbara McClintock had a "feeling for the organism" about maize, why, Ed had such a instinctive gestalt for the microbial world.

I once asked Ed about how to choose the right kind of textbook for teaching my single microbiology course.  His answer was pure Ed: "Three.  Two for you, and one for the students."  

And he was right.

Not only was Ed a living encyclopedia of microbiological wonders, he was irreverent and quietly funny.  I well remember a particular time at the general meeting of the American Society for Microbiology some years ago.  We were having a cup of coffee, chatting, and a very famous microbiologist brushed past us self-importantly.  Ed rolled his eyes and told me tales that would curl your hair.  You see, Ed didn't care where you went to school or what kind of position you held.  He cared about microbiology, and microbiologists.

After the Microbial Diversity course, Ed stayed in touch with me via e-mail.  I have dozens and dozens of e-mails from him, asking if I had seen a particular article.  Or had I thought about a new approach for my research that he had been reading about? 

And when I was denied tenure at Occidental College, Ed (like Abigail) was a rock.  As I live and breathe, I can never express enough thankfulness for that support.  Many, many people treated me poorly, or would not speak to me.  Ed Leadbetter acted exactly the same toward me, and when I was looking for new jobs, he had, um, colorful private opinions about each.  I trusted his assessments, of course, and had reason to do so.  

In fact, Ed invited me to serve on a PhD committee with him while he was at Woods Hole!  I suspect he knew I needed to feel like a professional, and his strategy worked well.  Ed would take me to lunch, and sit in committee meetings with pretty influential microbiologists---with me right there too, treated as an equal. Since I teach at an undergraduate institution, I do not have PhD students. So it was a wonderful thing to experience, and a kind thing for him to have done.

Even as Ed experienced health difficulties, he stayed in touch.  I adored getting his e-mails and reading his opinions on Matters Microbial™.  In fact, in the year before he passed away, Ed wrote to me to ask for a variety of tree leaves from our campus in Tacoma.  He was trying to look for patterns among fungi to be found on those leaves, and in typical Ed Leadbetter fashion, sent me a report on the "tree leaf fungi" on our campus.

This is how I will always see Ed Leadbetter in my memory.


The photograph is from his D.C. White Research and Mentoring Award at the General Meeting at ASM in 2014.  I was honored to have been asked to write a letter in support of Ed's receiving this prestigious award; having anything at all to do with that process is something that gives me true pride.  Ed Leadbetter is just that important to so many people, of course including myself. It was so impressive to see the myriad of people at his talk, and observe the affection and respect he received.  Ed was deeply moved by the award, as was the audience.

Over the years, I have discussed having Microbial Heroes™.  And let's face it, Ed Leadbetter must needs be a very bright star in that particular microbial firmament.  My talented and brilliant wife Dr. Jennifer Quinn made me a "shrinky dink" of Ed Leadbetter here.  It sits on my office shelf.  I'm certain Ed would have a rude response to my having it, but I don't care:  I thought the world of him, and miss him.


My wife and I also enjoy collaborating on "portraits made with living light"---that is, painting on nutrient media with bioluminescent bacteria, then taking photographs in the dark.  Here is the one we made of Ed Leadbetter.


But that wasn't enough for me.  I asked my artist friend Kaitlin Reiss to make a "microbial portrait" of Ed, and she did a fine, fine job.  Ed was all about the microbes, after all.

Kaitlin is also working on a similar portrait of Abigail Salyers.  I will get them framed above my computer.  

Ed Leadbetter led a life that mattered, and in so many ways, to so many people.  He certainly had a very large influence indeed on my own life.

Though I could not be at his memorial today in Woods Hole, I can promise Ed's friends and family that he is never far from my thoughts, and informs my classroom and laboratory every single day. 

I miss you, Ed.   Thanks for all you taught me.


Saturday, August 1, 2015

"Never Really Alone" with Ed Yong!

As I described a few days ago here, the new semester looms upon the academic horizon.  I feel "antinomy":  a mixture of contradictory emotions:  excitement (at the subject matter) and dread (of updating materials).  

But I will do my best to have fun, and engage students.

I will be teaching my beloved microbiology at the University of Puget Sound in the Fall with sixteen eager micronauts to whom I can proselytize the One True Faith of Microbial Supremacy™...but I will be teaching another course as well.  This latter course, which I call "Never Really Alone:  Symbioses and Parasitism Around and Within Us" is a freshman writing course.  It is intended to introduce new students to critical reading, discussion, writing, and presentations.  Here is the course description.



We were EXTREMELY fortunate last Fall to have some pretty remarkable people visit our class via "telepresence" (Google Hangout, Skype, etc) to explore student questions.

The second "telespeaker" we had last Fall was the indispensable Ed Yong:  science writer of Solomonic fairness and Monty Python-esque humor (and just recently, science correspondent for the Atlantic!).  His blog, "Not Exactly Rocket Science," contains truly top notch (and fair minded) science writing, and remains a honestly superb resource for students (Ed Yong has a skilled ability to "distill down" complex journal articles without losing the rigor or relevance).  Relevant to my course, Ed Yong has made several fabulous videos about the role that parasites play in animal behavior (a topic that ALWAYS grabs student attention most firmly):  here and here.

As before, I had students watch some of these videos, and read some of Ed Yong's essays regarding unusual parasites and changes in host behavior.  The students came up with questions.  I collated them and sent them along via e-mail to Ed Yong.  Then (and I am still quite grateful for this transatlantic conference!), he visited my classroom.  Enjoy!


Some of my students took to calling Ed Yong "that chill dude,"which I believe can be interpreted as high praise indeed.

As before, an artistic friend of a student in that class created "cartoons" of each speaker.  Here is the one of Ed Yong.



Finally, here is the "thank you" poster that the students created for him. 




It was an engaging and informative morning for the whole class, including emphatically yours truly.  I am quite grateful for all of the speakers, and wonder who I will get for this Fall to chat with my students!

More to come!

Wednesday, July 29, 2015

"Never Really Alone" with Jack Gilbert!

The new semester approaches!  

Gulp.

I will be teaching my beloved microbiology at the University of Puget Sound in the Fall with sixteen eager micronauts to whom I can proselytize the One True Faith of Microbial Supremacy...but I will be teaching another course as well.  This latter course, which I call "Never Really Alone:  Symbioses and Parasitism Around and Within Us" is a freshman writing course.  It is intended to introduce new students to critical reading, discussion, writing, and presentations.  Here is the course description.


Last Fall, I had quite a nice time with this course, and my 18 students.  Students seemed to like the course, and I know I did.  We were EXTREMELY fortunate to have some pretty remarkable people visit our class via "telepresence" (Google Hangout, Skype, etc) to explore student questions.

I am going to post those presentations in the next few posts, as I consider who might be willing to "visit" my classroom in the Fall!

The first "telespeaker" we had last Fall was the inimitable Jack Gilbert of the University of Chicago and Argonne National Laboratory.  I gave the students some readings relating to the work of Dr. Gilbert, and the students came up with questions for him. I sent Dr. Gilbert the questions, and he held forth!  

During his "virtual visit" to our classroom, Jack was his usual energetic and engaging self for the students.  Here is that presentation, which I highly recommend.



In fact, an artistic friend of a student in that class created 
"cartoons" of each speaker.  Here is the one of Jack Gilbert!



Finally, here is the "thank you" poster that the students created for him.  

Enjoy Jack Gilbert and his engaging style.

More to come!

Wednesday, July 1, 2015

EDAMAME, Michigan, and Metagenomic Analysis

“Aged Canids and Fresh Prestidigitation.”

There is a saying that “You can’t teach an old dog new tricks.”
So I am a bit of an unusual candidate for EDAMAME2015. 

First, what is EDAMAME?  It isn't the pleasant soybean dish often served in Japanese restaurants.  Instead, the acronym stands for "Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology."  It is a workshop for scientists, and one I very much wanted to attend.  The workshop, by the way, was funded in part by the generous folks at MoBio (who also provided course specific T-shirts).  This blog post appeared in a slightly different form on the MoBio website here.  

I am an older associate professor in the Biology Department at theUniversity of Puget Sound, and can even remember biology prior to PCR! At the same time, I have been following the recent blossoming of research into communities of microbes over the years, ranging from hydrothermal vents, to insect guts, to acidic cave effluent, to the ever present human microbiome.  Sociomicrobiology seems to be everywhere in science today, and I find the topic fascinating.

As part of my job teaching microbiology (the only such course taught at my small liberal arts institution) at the University of Puget Sound, I began introducing students to the concept of what kinds of microbes appeared to live in their reusable water bottles several years ago---at first via simple streaking and observation, to colony PCR with universal 16S PCR primers and phylogeny, and finally a tentative foray into next generation sequencing: real complexity.  This brought home central concepts in microbiology to my students, as well as applications to everyday life.

At the same time, I began to explore microbiology-centered research collaborations with two of my colleagues at the University of Puget Sound.  The first involved sex-specific differences in the cloacal microbiota of a species of lizard in Southern Arizona.  The second involved fermentation-generated seeps of hydrogen sulfide rich seawater in nearby Commencement Bay, resulting in microbial communities similar to those found at deep sea hydrothermal vents.  In both cases, it was necessary for me to better understand changes in the structure of microbial communities.  It quickly became clear that I lacked the tools and training.

I had been struggling for a while with these studies, with occasional help from patient scientists such as Jack Gilbert at Argonne National Laboratory. Progress was slow and frustrating. So when the announcement of EDAMAME2015 appeared, I decided to apply, despite the fact that I am, um, a quite a bit older and less experienced than most folks taking the course.

It has been a wonderful experience.  The lead instructor, Ashley Shade, was patient, supportive, and funny.  


The talented and friendly teaching assistants never once rolled their eyes at me as I learned about line commands, "the shell," the eternal quandary of QIIME versus mothur, Prokka, MG-RAST, and the arcane secrets of GitHub


The instructors never gave up on me, even when I sputtered to an intellectual stop regarding R. The instructors, and my fellow students, pitched in and brought me up to speed.  It was truly an educational community.

I tweeted out lots of highs from EDAMAME2015, such as my victories over mothur....



...and short-lived triumph over R.


The tutorial materials and experiences have certainly clarified much of what I am doing back in Tacoma, and given me a great deal of insight into improved approaches!  I think that, because of this course, I can finally feel more “in control” of my collaborative projects.  Also, I am thinking of how I might use these skills in my Fall microbiology course, letting each student analyze the microbial communities within their water bottles (funding permitting, of course)!  (Art work by my good friend Kaitlin Reiss).


After a long day of tutorials and pecking at keyboards, we were treated to quite an impressive array of seminars showcasing expertise relevant to the skills we were trying to learn or hone. The speakers included Vince Young , Jay Lennon, Stuart JonesAriane Peralta, Jim Cole, Sarah Evans, and Jim Tiedje. We had the chance to chat and socialize a bit with each of the speakers; what an opportunity!

Far from Starbucks, I quickly learned to relax in the slightly jittery but stimulating arms of graduate school coffee (note the two phase states of coffee provided).


There were surprises, as well.  I brought some of my own "Microbial Supremacy" stickers, and many participants wanted them (I always try to preach the One True Microbial Gospel™ wherever I go).


But I hadn't expected Pat Schloss to send along and distribute stickers for his bioinformatic program mothur.  The developers of another, similar, platform called QIIME, responded with stickers of their own.  Win-win from our perspectives!


I haven’t mentioned the nonscientific aspects of EDAMAME2015.  The course was located at the Kellogg Biological Station near Kalmazoo, Michigan.  And as the photographs below show, it is a lovely locale for learning.

Here is the Carriage House, where we feverishly learned each day.


There were lovely sites throughout the Station property on Gull Lake.


In addition, the weather was nearly perfect.


Did I mention the fireflies at night?


In addition, the students were diverse, warm, helpful, and welcoming. They enjoyed my tardigrade bottle opener.....


....and even made me microbially themed origami.


One night, we went on an expedition to a lovely brew pub in Kalamazoo. 


While on another night we enjoyed a great barbeque.


I believe that I have made some new friends and colleagues.
While I will be sad to see the end of EDAMAME2015 approach, I also know that I return to Tacoma armed with knowledge, skills, and a network of new colleagues who have already proved their willingness to help out people new to this area of research.

Yes, there is a saying that “you can’t teach an old dog new tricks.” In reply I would quote Henry Ford:  Anyone who stops learning is old, whether 20 or 80.”  So I did my best, and came away with more knowledge than I expected.

EDAMAME2015 was just the place to remind this particular aged canid that I can still learn and grow as a scientist.  And where better than with such a crew as attended this June?


It is truly a transformative experience for people interested in microbial ecology, and I highly recommend it as an intensive, positive, and unforgettable experience.