Tuesday, February 14, 2017

Happy Microbial Valentines' Day!

How about that January?  I know.  I do my best to just focus on my students and my research thoughts.

Today is Valentines' Day, and I would like to share some "bioluminescent art"---#LuxArt---for that occasion.  Again, I use Photobacterium leignothi strain KNH6, which I find to be very bright.  

First up, a salute to my beautiful and brilliant wife Dr. Jennifer Quinn.  Truly, she deserves every good thing (particularly based on her full time job putting up with my veering approach to reality!). Love you, Jennigirl.

Next,  there is nothing wrong with a bit of a Valentines' Day poem dedicated to my wife, is there?

How about a microbially relevant Valentines' Day haiku?

But no matter what, let's keep the next image in mind today.

My very, very best wishes to all of you.  And your microbiota!

May you be happy holobionts, one and all!

Sunday, January 1, 2017

The First Day of 2017

I have been blogging, irregularly, for several years here.  Some folks read what I write, most people do not. I am grateful for the former, but understand the latter.

This post is going to be different.  The first thing I want to say at the outset is that I am very lucky, and many people have far greater difficulties than I do.  That needs emphasis.

The past several years have been challenging for me both personally and professionally.  The death of my mother.  The death of my father. A fight to earn tenure at my current institution. A lack of research progress, and grant support.  Most recently, an attempt to be promoted to full professor being tabled in a way I find, um, a bit unfair.  So I have experienced some negatives personally and professionally.

Yes, there have been many positives, too.  My wife Jenny, my sons Anson and Zachary.  The continued successes of former research students (the most important thing I have ever done professionally is identify and mentor scientific talent in others). I have received some recognition and appreciation, especially off campus (it turned into an accurate joke with a former student:  I'm popular, but not in person).  

So why cannot these positive things outweigh the bad?

I would like to write about myself and my journey in this post. More importantly, I would like to write about how we all treat each other, particularly in these odd and turbulent times.  So:  no microbiology, no education, no students.  It's okay if you don't feel like reading more.  But I wanted to say a few things to people who might be interested.

I have suffered from depression for many, many years.  I say that with the full knowledge that I have much to be happy about, and a great deal of which to be proud.  I am well aware of the stigma that is attached to any form of mental difficulty.  That said, let me repeat:  I suffer from depression.  I work hard to hide it. 

Winston Churchill used to call depression his "black dog," and there is some truth to that.  This video explains things very well, I think.  It certainly struck powerful chords in me.

Given my challenges, it is remarkable I have come as far as I have; I certainly didn't expect that I would (i) get into a PhD program, (ii) complete a postdoc, (iii) get a job, (iv) return to academia, (v) have my career survive being denied tenure, (vi) get a new academic job, (vii) earn tenure at that new job, and (most of all) (viii) have my career survive all the spectacularly dumb things I have done over the years.

And I haven't even started on my personal life.  Yet there too, I have done far better than many.  I would say "better than I deserve," but that feeds into the whole self-deprecation thing again. Sigh.

Even with depression I survived all these things, did well, and am still standing.

We all know the story of the missing sheep. In a perverse way, I (and others like me) tend to focus on the negative.  To give more impact and credence to failures than to successes.  Worst of all for me is that I am very aware that my mindset is counterproductive. It's frustrating for others, and bothers the heck out of me, too.  

As an example, I dislike compliments and will minimize or negate them. I used to joke that my late mother was "psychologically Amish," because she would deflect or negate compliments.  To my mother, arrogance was a Sin among sins.  Arrogance is indeed unpleasant, but she took it too far, and so have I.

As you can see, my odd journey has impacted me in many ways.  I tend to understate my own abilities.  I avoid fighting or disagreements as much as possible---which I have found counterproductive.  I expect the worst from others (and from myself).  I see things illuminated by what I have called for many years "dark light."

I have let this affliction own me for many years, and yet I still have accomplished more than I objectively could have predicted.  I have trouble calling myself a winner, so perhaps I can call myself a survivor.  

I don't give up, despite all my complaining and negativity.  

So in the coming year, I will work very hard indeed to make some changes:  to be more positive, productive, supportive, and energetic.  I want to create the world in which I want to live---by being that person, and rewarding/encouraging those who think the same way.

When they were little, I use to joke with my sons that we needed a family motto:  we aren't problem complainers, we are problem solvers.

I need to take that to heart. 

We all---me included---need to change our ways.  Much of this is derived from the lessons we supposedly learned in kindergarten. I have seen a lot of hurt and cruelty, even in academic environments. Perhaps especially in academic environments.  The longer I am in academia, the more I see that Sayres was right.

True enough.  I often think we academics are the ones no one wanted on that fourth grade kickball team.  It explains a lot. 

It is true I have had to deal with some, um, not-fans of yours truly. It's a challenge to me to have people think poorly of me, and see me in the worst light possible. Still, there is some use in having folks like that around, to be honest: we all have room to improve.  My late father used to remind me that everyone in San Quentin Prison maintained that they were innocent; we all must own some of our own difficulties. We just need to find proportion.  And by "we," I mean "me." 

This is amusing and also true.

So what to do?  Persevere, again.  Not give up.  Not give in.  I do have supporters who think well of me, and I need to pay more attention to them. And I need to prove my detractors wrong, and rather silly, by my actions and example.  It's easier to just let things go and feel sorry for myself; energy is required to climb upwards into the light.  

When someone says or does something I do not care for, I need to stop.  Take a breath.  And then I need to ask myself:  do I do or say things just like that?  If so, I need to change.  Because the only person I can really change is myself.

There is a great book with an amusing title.  I recommend it to anyone in academia.  If you don't have time to read it, here is a short synapsis by the author.  

You see, bullying is contagious, even in academia.  It's all about folks in one group dissing folks in another group----just like middle school.  If you and your group are smart and good, why, folks in another group must be stupid and bad.  Again, just like middle school.

Few people (and no administrator) will stand up to most bullying, except in its most extreme forms.  It's easier to allow someone to be treated badly than to induce a bully to behave decently. So all I have is to take the better path.  To show by example I am not like that; to try to create the environment in which I want to live and work.  This is important for people other than myself; allowing bullies to do their thing---even in academia---leads to more bullies and less enjoyment in life.

And it's true in other areas than academia, as we all see.

But standing up has a personal cost, to me. My father used to tell me that the measure of a person was not how they treated people they liked or who treated them well. That was easy.  No, the measure of a person was how they treated people they did not like, and who did not treat them well.  

I want to follow my father's example.  It's not easy, but I am making progress.

In a larger context, here are some guidelines that might help create a better environment for us all.  They apply to me, too.

  • Tactlessness is not honesty.
  • Being overbearing is not the same as being forthright.
  • Cruelty to others is not a type of strength.
  • Kindness is not a form of weakness.
  • If you are talking, you are not listening.
  • If you are waiting to talk, you are not listening, either.
  • Be certain that what you call snark is not cruelty.
  • Avoid hypocrisy; if it is wrong when one person does it, it is wrong when another person does it.

I cannot speak for you, but hypocrisy drives me up a wall.  We all see people who have two sets of rules:  one for people they like (or themselves) and one for others.  I certainly see a lot of it on social media.  Sigh.  

Putting the proverbial shoe on the other foot is an important skill. People who believe differently than you do are not evil or stupid. But our internet world is all about snap judgement and narrative, so it seems to me....instead of about people, and the kind of environment in which most of us want to live.  

For me, the big take home lesson brings us home to Henry James.

And even to the late, great Randy Pausch.

I would encourage everyone to be kinder and more patient, as Henry James and Randy Pausch suggest. There is evidence helping others helps both parties, as the fearless Amy Alkon champions here.

I think she has a point. I believe that we should all strive to do one kindness for a stranger each day. And two kindnesses for people we know!

So the new year begins today.  I actually do have some resolutions:

  • Be less negative.
  • Be more grateful.
  • Get more sleep.
  • Get more exercise.
  • Become more organized.
  • Make things happen.
  • Do better research.
  • Get more papers published.
  • Blog more often.

Several scientists have offered to help me with the research part; another reason to feel lucky and grateful.  I intend to take them up on it.   It's time to bring that black dog to heel.  Wish me luck?

I may not succeed.  But I will keep trying.  And that is the one thing my life objectively demonstrates:  if you don't give up, and keep trying, you will arrive somewhere very near your goals. 

I will try to live by one of my old, old mottos:  
Loquere minus
Audi plus
Cogita semper
It means:
Talk less
Listen more
Think always
There is a saying I very much like.  "The future will not be as terrible as our nightmares, or as wonderful as our daydreams."

Finally, I want to wish each of you a wonderful 2017.  And I recently found a post by the essential and uplifting author Neil Gaiman (have you read his "American Gods"?) that is hopeful, positive, and genuine.  Here it is.

Notice the importance of kindness, again?

Ray Bradbury is another literary hero of mine.  Brother Ray speaks for me here:  I am fine being the person I am.  If some people don't like it, I would rather spend time around people who don't mind my quirks and talents.

Being yourself is important.

Brother Ray is also giving me good advice about my own future here.

If you will pardon me, I have some wings to build.  And many thanks to the folks who have offered to help me build them. I'm a bit of a group project.  As I get older, I am finally understanding that we are all group projects.

I'll settle for less anger, and more positivity, from me.  What about you? 

Saturday, December 24, 2016

Happy Luxmas to All!

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

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

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

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

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

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

As always, some #Luxmas fun.

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

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

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

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

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

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

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

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

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

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

Thursday, December 8, 2016

Microbiology, Student Learning, and Creative Extra Credit

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

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

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

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

And the results are gratifying.  

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

Erin created a Bacterial Phylogeny of Many Colors.

Mara created a mobile depicting the human microbiome.

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

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

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

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

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

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

Josh painted an epic bacteriophage.

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

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

Trini drew various microbes as "Micro-Avengers."

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

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


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

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

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

Tuesday, December 6, 2016

The Coolest Thing Bio350 Micronauts Learned in Fall 2016

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

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

Truly a moving target.

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

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

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

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

I remain a proud and unrepentant #MicrobialSupremacist.

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

First evolved, and last extinct, indeed.  

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

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

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

Sunday, November 27, 2016

Tests, Brave Micronauts, and Educational Art!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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