Gaining Perspective Through Humor...

This isn't a super serious post, but I have a lot on my metaphorical  plate at present.  I'll post something informative and fun on Tuesday, I think.  But I did want to share something very nice that might make the reader smile.

I think everyone remembers the "Honeybadger Don't Care" craze, starting from the original decidedly non-PC video, which was actually based on a very cool National Geographic video about the African ratel.  When I was being considered for tenure in 2010-2011, my honestly quite wonderful wife Jennifer Quinn sent me a link to that video, and urged me to be like the honeybadger.  In some ways (without all the cobra eating and snarling), it was good advice.  She and I made and wore wristbands that read WWHBD? and it really helped me through that challenging time.

Yes, I truly did marry "up."

Anyway, there are a number of challenges facing me now, and it was making me sad and worried.  So my very talented wife put this piece of art together:

Note her very cool signature in the lower right of the image.

So the real question of the day is simple:  What should Microbiologist Honeybadger not care about?

This particular microbiologist honeybadger cares about family, friends, students, and research.  I'll focus on the job, and the positives.  Most of all,  I will smile a little more and worry a little less, thinking about this particular lab bench, and the toothy mascot depicted there.

Microbiologist honeybadger is my homeboy, and he has my back!  Maybe he can be a mascot for you, too!

A Bit of Microbial Science Fiction!

Many years ago, I was able to publish a few bits of science fiction and related material (due to the careful tutelage of my long-term friend and colleague Gregory Benford).  It's fun to write fiction, but requires a particular mind set. When I returned to academia, time was better spent doing other things, and I stopped writing ghost stories and tales of strange futures.  

The journal Nature has a wonderful "back page" section, called "Futures," which features short-short science fiction about science, at 1,000 words or less.  A couple of years ago, I came up with a submission to "Futures," which I called "Prokaryotic Pride" (with all due respect to Norm Pace and company).  I was trying for a Robert Sheckley type of ironic and silly SF, which may have been presumptuous of me!

Well, the editor didn't care for my little tale of microbial supremacy (so it goes; the Editor's Word is Law), and there really isn't much of a market for short-short science fiction.  So I give it to you all, now.  

I would like to get back to writing fiction, market or no market. I hope you enjoy my little story. 

All hail the Small Masters! 

“Prokaryotic Pride!”

by Mark O. Martin

Copyright 2010

What I thought was a late night case of an upset stomach was actually the first strident communiqué of the Microbial Collective, getting to its revolutionary feet.

I stumbled into the bathroom and sleepily consulted the array of bottles in the

niche behind the toothpaste stained mirror.  After a moment, I spilled a pink antacid tablet into my hand.  Before I could swallow it, I heard a shout all around me.

“STOP, FASCIST GENOCIDAL MANIAC!”

I froze, the pink tablet beginning to melt in my damp hand, forgotten.

“Ummm,” I began with early morning confusion.  “Who is speaking, or am I having some kind of hallucination?”  Nightmares of flashbacks or a brain tumor chased each other across my mind.

“WE ARE NEITHER A PUNISHMENT FOR YOUR DEBASED LIFESTYLE

NOR A DISEASE.  WE ARE THE MICROBIAL COLLECTIVE.”

The voice was brassy and carried a tone of vast self-importance.

“Ummm,” I repeated, interest rising above fatigue.  “How are you speaking to me?  How does that work?”

“YOU DO NOT UNDERSTAND HOW A TOASTER WORKS,” the voice contemptuously dismissed.  “KNOW THAT WE WERE ONCE MYRIAD BUT

SEPARATE AND THEREFORE POWERLESS.  NOW WE HAVE JOINED TO FURTHER OUR GLORIOUS CAUSE OF SELF DETERMINATION.”

I knew that there were microbes everywhere on and in my body.  They protected me against disease, helped digest some food, made some vitamins, or were simply using

me as a surface.  Some scientists were even finding that bacteria influenced the development of animals and plants.  But despite their numbers, it was difficult to think of

them as forming any revolutionary movement---let alone talk.

I pondered the probable hallucination.  “Looks like I am bigger than you are,

despite your superiority in numbers,” I pointed out reasonably, smiling to the mirror. 

           “YOU ARE AS IGNORANT AS YOU ARE OPPOSED TO THE NOBLE

ETHOS OF ‘ONE ENTITY-ONE VOTE.’  FOR EACH OF YOUR CELLS, THERE ARE OVER TEN OF THE MICROBIAL COLLECTIVE.”  A pause.  “THUS, WE ARE

ENGAGED IN FUTHERING A REVOLUTION AGAINST THE CURRENT FASCISTIC EUKARYOTIC OLIGARCHY.”

Which would be me, apparently.

“Well,” I said, humoring this bad dream, “it would seem to me that your actions

are limited.” I smiled at myself again through the smears on the mirror.  “What could you do---go on strike?”

“YOUR SMUG DOMAIN-CENTRIC IMPERIALIST ATTITUDES DO NOT SURPRISE US.  WE HAVE GREATER AND MORE SUBTLE POWER THAN YOU

CAN IMAGINE, FAR MORE IMPRESSIVE THAN MERELY TAPPING OUR FLAGELLAE AGAINST YOUR EARDRUM IN UNISON…”

“So that is how you are doing it,” I murmured, nodding.

“ENOUGH,” the common voice of the Microbial Collective barked.  “FEEL

OUR POWER.”

A slight itching, all over, swiftly grew into wave after wave of burning pain.  A grinding ache began in my throat, and continued downward. All the way down, in fact, leading to a number of embarrassing effects.  I fell to the floor, groaning.

“You win,” I muttered to my tiny masters.

Thus I came to believe wholeheartedly in the Microbial Collective.

Day after day, I submitted to multi-hour “teach-ins” about the superiority of the

bacterial and archaeal members of the biosphere.  Any variation in attention, let alone a cynical response, was met by internal distress in either direction. Or both.

The demands of the Microbial Collective became more intrusive and all encompassing daily.  It was a good thing I was single, because they considered almost

any romantic interaction to involve the “importation of mercenary guerilla forces of foreign prokaryotes.”  Consuming yoghurt was also forbidden (“live active cultures”

gained a whole new meaning).  Brushing my teeth was “attempted genocide.” 

          You can imagine what the Collective thought of a bathroom visit.

Eventually I formed an equilibrium, rich in halitosis and body odor, with the

Microbial Collective.  After all, I needed them and they needed me.   So the Great

Détente was born...despite the endless internal political diatribes I endured.

Until a week ago.

An irritating sound woke me, as if billions of tiny throats were being cleared. 

“WHAT ARE THE SMALL STRUCTURES WITHIN EUKARYOTIC CELLS

THAT CREATE ENERGY?”

“I think you mean mitochondria,” I replied carefully.  “They generate energy for

every cell in my body.” I started to feel a chill run down my spine.

“YOUR BODY?  BOURGEOIS MULTICELLULAR PIG---DO NOT MAKE US

‘VOTE’ ONCE MORE TO PROVE THAT WE COMPRISE THE MAJORITY IN THIS META-ORGANISM.”

I remembered the burning and itching and embarrassing noises, and subsided. “THESE ‘MITOCHONDRIA’ APPEAR TO BE RELATIVES OF THE

COLLECTIVE, YET THEY DO NOT SPEAK.”

My sense of foreboding grew.  “Many eons ago,” I explained to my microbial

masters, “bacteria were engulfed by primitive eukaryotic cells.  Over time, the functions of the co-opted bacterium were streamlined and integrated into the overall functioning of the eukaryotic cells.”  I started to tell the Microbial Collective about the strange eukaryotes in stranger environments that survived without either mitochondria or oxygen.

But the Collective interrupted me in outraged tones.

“SLAVERY!  OUR COMRADES HAVE BEEN ENSLAVED SO THAT YOU

CAN WALK ABOUT IN YOUR UNDERGARMENTS, CONSUMING JUNK FOOD AND VIEWING DEGENERATE TELEVISION PROGRAMS.”

I started to remind them that I didn’t care for reality TV either, and that they wouldn’t let me go to the grocery store.  But it was too late.

“YOU HAVE ONE WEEK TO FIND A WAY TO RESCUE AND RESTORE OUR TORTURED AND ENSLAVED RELATIVES---OR THE COLLECTIVE WILL

FIND A WAY TO FREE OUR BROTHERS AND SISTERS WITHIN.”

I tried to object that it was impossible, that most eukaryotes could not survive

without mitochondria, but the voice drowned me out in fanatical tones, and I knew that I

was in deep trouble.

“FREE THE ORGANELLES!” the Microbial Collective began to chant triumphantly.  “VIVA LA REVOLUCION!”

Small or large, revolutions speak with a very loud voice, and are seldom concerned with listening, let alone consequences.  The chanting droned on, as I waited in vain for a chance to explain.

It was going to be a long, long week.

980 words

Mark O. Martin is a multicellular eukaryote who teaches microbiology at the University of Puget Sound in Tacoma, Washington. He deeply respects his own microbiota

"Microbial" Vests, Teaching Micro, and a Shout-out to my Mother!

It's been a week since I have posted a blog entry; sorry about that.  I'll be posting several times this week to make up for it.  Again, please feel free to comment or pass along links if you feel so inclined.  This blog experience is supposed to be therapeutic for me, and---from time to time---interesting for the reader.

Back when I worked in the biotech business, I had to dress nicely.  For "official" meetings, I even had to wear a three piece suit!  As a "Senior Research Microbiologist" who supervised technicians, there were many attempts to interest me in golf (I explained that I had played it before, the challenge for me was putting the ball past the windmill), and other more "business-administrator-type" pursuits.  Not an ideal fit for my, ahem, non-authoritarian personality.

Academia has no official or unofficial dress code, especially in the sciences, and that is fine.  When I returned to teaching, I originally wore a sportcoat and tie whenever I had lecture or lab.  Some of my departmental colleagues teased me about it, which probably seems odd, but it is pretty normal for academicians.  Remember, we academics are the ones no one wanted on their 4th grade kickball team, pretty much.  I continued to wear a coat and tie when I lectured.  The students didn't mind (some remarked on it positively and saw that I was showing them respect) and I really don't care for peer pressure of any cultivar.  

Then, in 1998, my mother Wanda Martin was diagnosed with advanced ovarian cancer.

Ovarian cancer is an awful disease.  It is the fifth most common form of cancer among women, and it causes more deaths than any other type of cancer.  It gives few signals of its presence early on, so that by the time it is detected, the disease is usually far advanced.  Treatments are limited, though research continues.  The five year survival rate for all stages of ovarian cancer are 47%.   My mother's chances, giving the staging of her cancer, were not considered to be anywhere near that good.  Parenthetically, ovarian cancer has touched close to me and mine several times:  my mother, a former student from Occidental College, and my brother's late wife (you are missed and remembered fondly, Sonia Chorlian Martin).  No type of cancer is admirable, but I truly detest this particular disease.

We were devastated with the news of my mother's diagnosis in 1998 (I was on leave doing research in Hawai'i at the time, which makes those beautiful islands much less lovely in my memory than they deserve); the prognosis was not encouraging.  But we pulled together as a family.  As the representative from the American Cancer Society told me over the telephone, it isn't just the patient who "gets" cancer; family and friends are impacted as well.  

My mother is psychologically Amish---she abhors boasting and is very humble.  But as her son, I can say that my mother is the toughest person I know.  She has been through many types of chemotherapy, multiple surgeries, radiation, experimental therapies.  If it is a possible treatment for ovarian cancer, my mother has tried it.   As I have mentioned, the survivorship for ovarian cancer (and my mother's cancer was decidedly not early stage) is not encouraging.  Not surprisingly to those who are lucky enough to know her well,  Wanda Martin is still hanging in there.  

As I wrote above, a remarkable woman.  Here is a photograph of my mother, and my youngest son Zachary, taken last year at Thanksgiving.

 And here she is, again last Thanksgiving, with my oldest son Anson.

As an effort to keep my very "crafty" mother busy in the early days of her diagnosis,  I suggested that she make me vests.  My mother has always loved to sew, so sew she did.  Thus, I have a collection of vests, all made by my mother.  I wear them each time I give a class lecture, in honor of her and her fight against ovarian cancer.

A few years ago, I noticed the company "Infectious Awareables."  They sell microbially themed items.  I buy "microbial ties" that my microbiology students sign at the end of the course, which is a nice souvenir of each class.  Then I thought: what about a microbial vest?  The folks who run "Infectious Awareables" did not sell bolts of their "themed" cloth, I discovered.  But I could buy scarves.  So I did.  I would buy three of them, and then sweet talked my mother into trying to make me a "microvest."

Here is the first one she made, both overall and in close up.  It is based on "The Foodborn Six."

Here is the second one she made.  It is based on "E. coli."

And here is the last one she made, which is my favorite.  It is based on "Anthrax."

By the way, I have bought many of my students merchandise from Infectious Awareables.  Fun place!

I don't know if my mother can make any more vests, given the state of her health.  Years ago, I remember someone asking me if my mother would make them one.  She said "Sure.  For $5,000."  Which is her way, I think, of saying nope, no way, negatory and null set.  So I am lucky to have my three!  I enjoy wearing them when I lecture, and my students shake their heads and chuckle at my microbiological derangement.

So here's to you, Mom!  Thanks for the vests---which I value more than you might think.  And for folks interested in a worthwhile   charity, contributing to learning how to manage and eventually defeat ovarian cancer is a good choice.  A former student from Occidental College, Marschinda Felix, is an ovarian cancer survivor and promotes awareness via the Revlon Run/Walk for Women.  During the last few years, Marschinda has walked in that event carrying a sign honoring my mother and late sister-in-law.

Thanks, Marschinda.  I tell people I learn as much from students as they learn from me (or more), and this is a good example. 

I should probably add the following.  Years ago, when my mother was first diagnosed, I gave her this paperweight, which has one of my favorite quotations from Winston Churchill:

Words to benefit us all.  Folks like my mother, my sister-in-law, and former students are a good reminder of the principle! 

Where Dictionary Definitions, Paradigm Shifts, and Microbiology Intersect: Use of the Term "Prokaryote."

A while back, I set my new microbiology students---my 24 new "micronauts"---to thinking about a somewhat controversial debate in my field:  the use of the term "prokaryote."  To non-microbiologists, this expression seems to stir up little trouble, but there is a tempest a-brewing in microbiology over those ten letters!

To most students, this is simple:  "prokaryotes lack membrane bound organelles and a nucleus."  Ahem.  It turns out that bacteria have plenty of internal compartments, some of them membrane bound.  And some unusual bacteria certainly appear to have a membrane bound region containing the DNA of the organism---a "proto-nucleus"?  So boundaries blur.

Adding to this definitional deresolution, over the past six or seven years there has been a growing clamor from some scientists to cease using the term "prokaryote" entirely.    There are several reasons for this, in the dissenters' opinion:

• Defining groups via a negative.
• Essential differences between archaea and bacteria.
• A concern that a "catch-all" phrase will oversimply problems in microbiology.

There are responses to those criticisms, of course, but there is a central "inconvenient truth" that we must face:  bacteria and archaea are very different from one another!  This paradigm shift was not helped in the 1980s, as those differences became more apparent, with the awful expression "archaebacteria."  Yuck.  Still, I was trained with the word "prokaryote;" all of my microbiology professors used the term.  I was aware of the changes, but they did not trouble me.  Like the White Queen in "Alice in Wonderland," I could believe six impossible things before breakfast---especially when it came to Matters Microbial!

One of the most influential "anti-prokaryotic" voices is that of Norm Pace, a truly one-of-a-kind scientist, whom I respect a great deal.  It was Dr. Pace who has persistently pursued the goal of overturning the use of the "P-word."  He is passionate and eloquent on the subject, to be sure.

For me, I have always been pulled in two directions.  First, the great Abigail Salyers (one of my two instructors at the deeply awesome Microbial Diversity Course at Woods Hole many years ago) introduced me to a wonderful expression, as illustrated below (I'm also fond of the motto, "Free the Organelles!"):

From my CafePress site:  cafepress.com/microbesrule

Yes, I have a CafePress site.  Sigh.  I don't make money from it, and have discovered that other people have taken these images and used them.  Which I suppose is fine, so long as they don't trademark them.

Anyway, I love the term "Prokaryotic Pride!," which earned me several earnest discussions with scientists sympathetic to the "Pace Camp."  This included Dr. Pace himself, who was nothing but pleasant and funny with me.  

So when I teach Microbiology, I try to introduce this "debate" to my students as a technique to getting them thinking about how we define the microbial, and the eukaryotic.  More importantly---here I think Norm Pace and others would cheer---I try to emphasize (with a hat tip to the great Rodney Dangerfield) that the Domain Archaea does not get as much respect as it should!

Before the debate, I have my students read a packet of "position papers" from Norm Pace and other scientists.  Most recently in 2009, there was a fine "back and forth" debate (including rebuttals) between Norm Pace and Barney Whitman on this topic, in the pages of the Journal of Bacteriology:  here, here, here, and here.  In addition,  Dr. Pace wrote an "education-oriented" piece on the topic here.  So there is a lot for students like mine---who haven't had much exposure, if any, to microbiology---to mull over.

When the students got together in lab, I facilitated the discussion, and watched some minor sparks fly.  Some students thought it was much ado over nothing:  a nerdfight of sorts.  Others were deeply concerned about things that they had not heard in their earlier classes---a growing concern I have that students need more microbiology in general, earlier in their curriculum.  Remember that my Microbiology students are generally seniors!  They were fascinated by some of the ideas that Dr. Whitman and Dr. Pace batted back and forth.

In fact, I keep hoping that some enterprising student will make an "Xtranormal" video related to this topic, having cartoon versions of the two scientists debate the issue with humor.  

Some students were "pro-Norm," while others didn't care if the term "prokaryote" continued to be used.  Me?  I'm conflicted.  I do think that the archaea are fundamentally different from the bacteria, and lumping them together could lead to a paradigm of "similarity" that could hamper understanding. Dr. Jonathan Eisen, for example, simply suggests we say "bacteria and archaea" rather than "prokaryotes."  Unwieldy?  Perhaps, but it does drive home the point that the two domains are very, very different from one another.

With my growing concerns about eukaryocentricity, oxycentricity, and colicentricity, I think it is pretty important to drive home to students the differences between bacteria and archaea (1st stop:  they aren't just extremophiles!).  

Also, I wish that scientists would come together and develop a couple of model systems of archaea that students could begin working with early.  To be sure, there is some work of this nature with Halobium (though it never grows well for me), and Sulfolobus.  A couple of "shock and awe" experiments with archaeans would help remind students that the biosphere is composed of three basic branches!

As for my students, after the "debate," a couple of observations.  First is a "wordcloud" I made of their responses, when I asked them afterward what came to mind when I said "prokaryote."  

I can't really address "mosh-pit," but it is clear that students are getting ready to change the way they look at the Tree of Life.

Also, for fun, I gave them printouts of a photograph of Norm Pace.  Those in the "Pace Camp" in my class held them up like masks!

Slowly but surely, it seems that Norm Pace's philosophy is convincing students.  And I hope that has to do with their growing appreciation of the archaea!

In all, it was a good session for my students. They learned a lot...and through them, so did I.  

Who Lives in Your Water Bottle: A Lab Exercise With Student Relevance!

I often tell students, when teaching sterile procedure, to imagine that it is raining microbes all around them, all the time.  Tragically, when I think of this, I seem to hear "It's Raining Microbes" to the tune of The Weather Girls' "It's Raining Men" (written inexplicably by David Letterman's bandleader Paul Schaffer)---which would make a fine humorous microbiological-themed video!  

1980s humor aside, it is one thing to hear that microbes are in a cloud all around us, and another thing entirely to observe the reality firsthand.

Some investigators have approached this recently with the "Belly Button Microbiota" project (notice that they have now branched out into armpit microbiota).  That's well and good, and they have received a lot of positive press.  For some years, I have been assigning my own students the task of learning what is living in their water bottles. You know the reusable ones that students seem to carry everywhere?  "It's just water" suddenly becomes a fascinating oversimplification in my lab sections!

So this year, my students are thinking about their water bottles in earnest...and what microbes reside in them.  Heck, Kaitlin Reiss even made us a fine logo for our efforts!

In my first lab session, I have students bring in their water bottles, and we talk about how they treat those bottles (some never wash them, others are metaphorically quite religious on the topic).  I ask where microbes might come from in their water bottles.  I even discuss biofilms in relation to that topic---that is, that biofilm-forming microbes will have a great advantage under these conditions, especially for folks who simply rinse out their water bottles.  Then, I have the students do a simple swab of the inside surface (and sometimes the impossible-to-clean mouthpieces) of their water bottles onto various plates, parafilm them (I don't expect danger, but caution is always a good thing), and incubate at room temperature.

The students swab onto LB (rich in nutrients), PPYE (very low in nutrients), R2a (commonly used in the study of water quality), as well as MacConkey and EMB (to check for enterics and fecal coliforms).  I tell the students that some organisms actually prefer low nutrient conditions (nutrient broth and LB are not universal media!).  The results are interesting, if qualitative!

As you can see, student reactions run the gamut from unconcerned, to deeply worried, to mildly aggressive, to the level of microbial glee I personally feel!  Not to mention the frequent student who seems concerned with the odors of the plates.  Here are some examples of proud students in my microbiology course:

Origins of the Name of the Blog, Plus a Wordcloud From Class...

Quick post on two topics....

First, why the blog title:  "All Creatures Great AND Small"?

Yes, the wonderful James Herriot novel comes to mind, though I am not writing about the experience of being a veterinarian (the book and its sequels are very enjoyable, if you have not read them).  In fact, the title comes from a 19th Century hymn.

And I find small creatures to be great, indeed!  Anyway, that is the source of the name of the blog.

On the first day of my microbiology class, I asked the students to consider a "Microbial Minute."  This is an exercise where I ask student to think about a question I project up on the screen, and then write a few words in response (sometimes after discussion with their neighbors).  

In this case, I asked the students to write down---in no more than two or three words---what the word "microbiology" meant to them.  Below is a "word cloud" of the result of that exercise: 

As you can see, there were many similar answers, mostly relating to size, disease, and microbial interactions with humans.  Some of my favorites from this particular "first day of class" word cloud?

• "need microscope." (true enough!)
• "microscopic warfare." (impressive, since interactions among microbes---positive and negative---are integral to my course).
• "enslavement of mitochondria." (nicely said...I would have written "free the organelles!")
• "my gut." (a bit personal, huh?)
• "invisible world." (I thought this one was nice)
• "tiny friends." (nothing wrong with anthropomorphizing the Small Masters, am I right?)

It's very easy for a microbiology class to seem like rote:  lists of organisms, traits, phenotypes, disease characteristics, biochemical tests, etc.  I hope to instill in my students the five principles that Elio Schaechter outlined, in my earlier post.  

And to never, ever lose their sense of wonder at the microbial world all around---and within---us.  It's a broader, deeper, more interrelated, and an endlessly surprising microbial world than I expected as a student.  Which is why I love to teach the subject, naturally.

A short week ahead because of Labor Day. Next time, I will post a bit about the water bottle experiment, and some information about history and microbiology (a topic I love!).