Tuesday, December 24, 2013

Merry Microbial Holidays!

It's been a semester with a veritable roller coaster of ups and downs, both personal and professional.  But honestly, I am more lucky than not.  I hope that each of you can say the same.

I'm in the process of writing two posts about my wonderful Microbiology students this past Fall semester (wait until you see their "creative extra credit" assignments!), but I am (as usual) behind schedule.

Since it is Christmas Eve as I write this post from an airport, in between several flights to visit faraway family, may I offer every one of you my best wishes for a Merry Microbial Holiday season?



Many, many thanks to my lovely and talented and brilliant wife Dr. Jennifer Jean Quinn for putting this video together a couple of years ago from a series of photos I took.  Of course I have bioluminescent ornaments for my "Microbial Luxmas Tree™"!

More later!  I cannot wait to learn about what new and exciting microbial discoveries await in the New Year!

Sunday, December 8, 2013

Another Sad Passing of a Microbial Hero™----RIP the Late, Great Abigail Salyers...

My colleague Jonathan Eisen, on Twitter, has often referred to people in microbiology whom he admires as "Microbial Heroes." I think he should trademark that label!  I have known many people whom I consider to be a Microbial Hero™(and yes, Jon, there needs to be a T-shirt made listing them all!).  But it is very sad to see any of these people---some of whom make seminal contributions to the field of microbiology, others whom are inspirational teachers and mentors, and some of whom are both---pass away.

The poet Rilke wrote, long ago, that "death is large" (it's better in German:  "Der Tod ist groƟ").  Some people begin to experience the losses that death brings at an early age.  For others, it is a sobering and sad characteristic of growing older.  It can be personal, as happened with my mother last year, or friends over the years.  Or it can be someone famous and influential to one's field of study, as the loss of the late, great Carl Woese last year.  Definitely a Microbial Hero™, and then some. 

And it can be a beloved teacher and mentor, someone who had a genuine and deep impact on one's life.  Thus, I was deeply saddened by the recent death of Abigail Salyers.  She too is a Microbial Hero™ of mine, and one whom I will never forget.

I have loved microbes since college (well, before college, actually).  And after I left biotech and returned to academia, I was lucky enough as a somewhat well-aged assistant professor to take the Marine Biological Laboratory's "Microbial Diversity" course at Woods Hole Massachusetts, in the summer of 1996.  It was taught by Abigail, and the great Edward Leadbetter (yet another Microbial Hero™ who has been very influential in my life).  Here is a photograph of that course, taken way back in 1996 (I'm in the top row, second from the right...as the saying goes, time doesn't fly; it flees!).


Anyway, the Microbial Diversity course literally changed my intellectual life---both in the lecture hall and in my undergraduate based laboratory.  I cannot easily or completely express how everything changed inside my head regarding Matters Microbial. And I have Ed---and Abigail---to thank.  Truly Microbial Heroes™, and not just to me.

I don't feel quite right singing all of Abigail's praises, since my knowledge of her life was limited.  Trained originally as an atomic physicist, Abigail then moved into microbiology (and the genetics of microbes living within the colon, as she un-embarrassedly and humorously insisted on telling people).  From there she published a remarkable body of research, several books, and influenced many, many scientists and students (including yours truly).  Abigail was even a past President of the American Society for Microbiology

I found Abigail to be a whirlwind of ideas, irreverent humor, and practicality. I would emphasize her humanity about all things (which makes sense when you read about her early life, as I hope you will).  For example, when my first academic job, um, did not work out, Abigail offered to help me out financially.  This was remarkable, since I had taken the Diversity course with her, and stayed in touch via e-mail---but I was not a student of her, nor what I thought of as a close friend.  But, as she put it to me in an e-mail, we were colleagues, and colleagues were in the business of supporting one another.  Abigail was one of the people who seemed as pleased (or more so) as I was when I finally earned tenure.  

On a more personal note, two of my former undergraduate researchers, Robert Jeters and Jillian Waters, earned their PhDs with Abigail.  I didn't worry a bit when they chose her lab; I knew that they would receive the training, mentoring, and support any PhD student requires.

In any event, many others who knew Abigail better than I did have written about her eloquently elsewhere. The great Elio Schaechter of "Small Things Considered" did a nice remembrance here, for example.  There is also a truly wonderful "must listen to" interview with Abigail here, that showcases the depth, breadth, and humanity of this remarkable and much-missed woman.  

In the aftermath of Abigail's death, I read the following poem written by the husband of one of her technicians and colleagues, Nadia Shoemaker.  The acrostic says it all about Abigail Salyers, far more elegantly than I can.  

While I took the Microbial Diversity course in 1996, I had the chance to share several meals with Abigail. During that time, she and I discussed how bacteria and archaea "don't get no respect" (to borrow from the great Rodney Dangerfield) in the public eye, and even among many biology majors.  If you don't believe me, ask students to write down the first thing that pops into their heads when you say the word "bacteria."  

Anyway, Abigail and I decided that microbes needed a motto, even a PR strategy.  So she and I came up with the first serious pro-microbiology slogan I ever used in the classroom, as you can see below (thanks to my artistic mathematician wife Jennifer Quinn for the original artwork, quite a few years ago!).



Abigail and I even came up with an alternative motto:  "FREE THE ORGANELLES!"  Abigail liked this slogan campaign (and was polite about my other approaches toward pro-microbe PR over the years).   

To be sure, Norm Pace and many other microbiologists encourage the abolition of the term "prokaryote" as can be seen here (I actually put on a debate in my microbiology classroom each year on this topic, in deference to Norm Pace's ideas).  Fair enough. Attractive alliteration aside, "PROKARYOTIC PRIDE" will always remind me of the person I used to call "Hurricane Abigail."

Abigail Salyers entered my life like a hurricane in Woods Hole, causing a storm of new ideas and paradigm shifts to enter my teaching and research.  I owe her a great deal, and I can only try to repay that debt forward.

One final note.  My personal style tends toward the, ahem, flamboyant during job interviews and in the classroom.  My PhD advisor urged me several times to "dial it down" when I was out for job interviews, and a very trusted colleague told me several times to be "less Markish."  Ouch.

I mentioned this to Abigail during my last job search, eight years ago.  She was pleasant as always, but a bit impatient with me.  "Be who you are, not someone you aren't," she commanded me. "Imagine if you pretended to be someone you weren't? What an awful way to spend your life!" Then, echoing the great R.P. Feynman, she asked "What do you care what other people think? Do what you think is right.  Stick to your guns."

What if I was too unusual?, I asked her.

Abigail replied with an impolite word.  "Then those are places you would never be happy," she insisted.  "Own who you are, and use it to do the best job you can."

I have tried, Abigail, and will continue to do so.  I will continue to use the advice you gave me, and the example you have been, to help others and improve my craft.  Rest in peace.

Readers, I was lucky:  I enjoyed the privilege of having Abigail Salyers as an instructor, and a mentor.  I miss her already.

Saturday, December 7, 2013

Rules for Academics (and "Martin's Laws of Research"!)

Over the years, I have made an embarrassingly large number of mistakes as I progressed through academia.  Some are normal mistakes, and others are quite cringe-worthy.  Gulp.

Don't get me wrong:  I did manage to get to where I wanted to be in academia, but it was a near thing, and took me a couple of attempts (I am not cueing the Violins of Infinite Sadness™; I am delighted to be here and grateful for the combination of fate and good luck that put me here).  In most cases, my problems were entirely due to my own choices. Okay, maybe it was a 50-50 split, but I do not wish to avoid my own responsibility for my, um, non-strategic and decidedly non-optimal decisions.  One of the things I try very hard to teach my students is the concept of ownership; it's critical in life, and took me a long time and much pain to learn.  

I don't have a time machine to go fix anything I did or did not do in the past, but I have learned a few hard-won lessons during my veering ride to where I currently sit with tenure at a small liberal arts institution. Thus, I have some "rules for research" I would like to share.  In addition, I also have some information from a former colleague of my wife Jennifer Quinn's at the University of Washington-Tacoma that I would like to share.  This is the kind of thing that all of my research students have heard repeatedly, of course, but I would like to share these thoughts with any readers of this blog.

The rules are not necessarily complete, nor do they necessarily apply to everyone reading this blog post.  One size emphatically does not fit all (boy, is that ever a rule for life)!  Still, I think it is important for any academic to think about these rules, and maybe to pass them along to other academics or folks considering a career in academia. 

First, some genuine wisdom from my wife's former colleague at the University of Washington-Tacoma (Beth Rushing, former Vice Chancellor for Academic Affairs, currently Vice President for Academic Affairs and Dean of Faculty at St. Mary's College of Maryland).

"Five Things I Wished I Had Known When I Was Beginning as a Faculty Member" 
1. There is a hierarchy among faculty members. Respect it.
2. You can be friendly with students, but they are not your friends.
3. Sometimes you have to say "no," close the office door, and/or work at home.
4. Everyone's job is important. Be nice to the staff in your program.
5. Your job is not your life.

These rules are perceptive and painfully true. Rule #2 in particular always cuts me to the quick. It is true that some students can become friends, but not initially.  It's a power differential issue, essentially.

And I am continually surprised by the number of academics who don't "get" Rule #4.  We are all supposed to be on the same team. Over and over again, I have seen academics seemingly look for things to fight about with colleagues and staff, which I guess take me back to Rule #1.  I think Marcus Aurelius had the best response to this issue:  "The best revenge is not to be like your enemy." Too often, we become the very things we claim to detest!

If I were to add anything to this list it would be simple: stand by your ideals in a calm fashion. We all have trouble with disagreements; learning how to be civil about dissent is an important and very useful skill.  It is also a rare skill in most human interactions!  I highly recommend this book for folks in academia.  It has a jarring title, but there is a great deal of truth in it, and it is very much worth reading.

From my perspective, there is a difference between honesty and tactlessness; many people confuse the two.  In addition, rudeness is not the same thing as strength, nor bravery.

Anyway, I like Dr. Rushing's rules.  According to my wife, they were taped to Dr. Rushing's office door while she was teaching and being an administrator at UW-Tacoma.

Me?  I have a few rules I have learned as I worked my way through academia.  Here they are.

"Martin's Rules of Research" 
Rule #1: There is one ego per lab (and it's not yours). 
Rule #2: Research projects sometimes appear to actively resist investigation (I take it a little personally).
Rule #3: Never forget that there is a "re" in the word "research." If you cannot repeat the experiment, it isn't science.
I teach all of my undergraduate research students these (and other) rules, and have some of them on plaques posted in my little laboratory.

For example, I have this famous quote up---it's very important for the most jaded among us to remember.


Absolutely.  That is what is so very cool and frustrating about science, in my opinion.  No other job is like it.

My Rule #1 is a maxim that few undergraduates "get," but it is painfully clear to anyone who has worked on a PhD.  Again, I cringe when I think about my own experiences, and that particular rule.  But sometimes the most painful rules are the ones that have the greatest influence on a person's development.  Still:  ouch. Needless to say, I do not have a plaque with that lesson posted!


Most of us doing research can appreciate Rule #2.  One can get very paranoid about this while working long hours at the bench.  I know I have, and only grudgingly have relaxed about such things. The little plaque under my sign is a gift from a former student of mine, Robert Jeters.  I used to put it outside of my laboratory, but people kept taking it.  So perhaps I now mean it is safer inside my lab than outside! 


Rule #3 is so very important, in my opinion.  I well remember a student in my lab many years ago excitedly telling me that she had a great result from an enzyme assay.  "Great!" I replied.  "Now it is time to repeat the experiment twice more."   The student looked confused. Years later as a postdoc, we had dinner and laughed about that incident.  The scientific method is both simple and unforgiving; at its heart is the necessity that others must be able to repeat your work!

This reminds me of the great Tiffany Ard's poster showing how toddlers inherently understand the scientific method and hypothesis testing.  I have her humorous poster depicting this set of cosmic truths up in my lab, in fact.

Honestly, I feed fairly low in the Trophic Web of Science. But I have watched many of my former undergraduate research students become wonderful scientists, and I hope that some of what I have tried to teach them has stuck with them, made them smile, and hopefully become part of their own world view and laboratory.

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