Friday, June 28, 2013

Stop Action Video, Bdellovibrio, and My Brilliant Spouse!

Summer research, paperwork, parental duties, family life.  It's a juggling act.  Things move quickly (I often say:  "Time doesn't fly; it flees").  I have some interesting ideas for microbially-oriented posts on this blog, but I need to get past this current tsunami of paper! Until then, here is something that happened today that is a lot of fun.

In my undergraduate-oriented research laboratory here at the University of Puget Sound, I work with students on several microbiology-related projects.  I have long had an interest in predatory microbes, including the wonderful and wily Bdellovibrio.  

Bdellovibrio has an interesting life cycle.  Free swimming "attack phase" cells swim very quickly  (up to 50 cell lengths per second) in search of prey.  When an "attack phase" cell contacts the "correct" prey (pretty much any Gram negative bacterium), it quickly enters the periplasm.  Swiftly, the predator modifies the outer membrane of the prey so that subsequent Bdellovibrio attacks do not occur readily.  It also begins to degrade prey cell macromolecules swiftly and quite efficiently.  The invading Bdellovibrio (nestled within the prey cell periplasm) causes the prey to "round up" into a structure called a bdelloplast.  After several hours, the depleted prey organism bursts, releasing a number of progeny Bdellovibrio cells.  And the Circle of Predatory Life™ begins anew.

It sounds like a super-bacteriophage, but in fact Bdellovibrio in attack phase has an extremely high metabolic rate as it chase prey.  So until we find some kind of girus with innate metabolism, this remains a good rule of thumb to exclude that "super virus" thinking.

Some researchers are beginning to think of Bdellovibrio as a "living antibiotic," and have begun investigations in chickens and other systems to see if the predator could be used to reduce pathogenic bacteria during infections.  

It's a challenging system with which to work, especially with undergraduates.  I have long loved working with "undomesticated microbes" but they do seem refractory to cool and simple molecular techniques.  I take it a little personally.  But Bdellovibrio is fascinating.  And my wife Jennifer Quinn, who is not only a brilliant mathematician but quite a creative artist, made the following "stop motion" video for me, using her iPad, an app called "Stop Motion," iTunes, iMovie, Play-Doh, and a whole lot of creativity:

I hope you enjoy her video as much as I did.  And keep in mind that microbial predation is quite widespread in nature.  Which brings us back to Jonathan Swift:
So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite 'em;
And so proceed ad infinitum.
(from:  Poetry, a Rhapsody)
It's true that Swift was referring to editors in this very long poem, not predatory bacteria.  But Bdellovibrio is still a fascinating, fascinating system.  And predators and prey continue to do their coevolutionary dance, even among the tiniest of creatures!

Saturday, June 15, 2013

Being a Father and Thinking About My Father on...Fathers' Day.

Wow, but it has been a busy summer this far!  Anyway, this post doesn't have a thing to do with microbiology.  Directly.  

June 16th is a very special day to me, and crowded with events.  It is "Bloomsday" from James Joyce's quite unusual novel "Ulysses."  Everybody seems to get in on the Joyce-ian act for that day, such as here and here.   It is also my birthday, which is less and less important to me with every passing year. In addition, it is my parent's anniversary, which seems to be growing in importance to me since my mother's death last October.  And this year, it is also Fathers' Day.  This is probably the most important holiday on that list for June 16th this year, since being a good father is vital, even if we fellows fall short of the goal from time to time.

So I would like to write a few words about my father, Jack Sevard Martin, Sr.  

My father was born in Marysville, California in July of 1931.  He was raised on a small farm, and took care of chickens, milked cows, butchered pigs, picked peaches, and helped feed his family during the Great Depression.  He was too young for World War II, and narrowly missed being drafted into the Korean War.  There is something of the soldier in my father, regardless.  In 1951, he married my mother, Wanda Jean Burton.  

When my father was fourteen, he had to start helping out at home to pay his way, and thus began going to school in the day and working at night.  My father was always, always about the work ethic.  As a boy, he worked as a ticket seller in a theater.  Cleaned floors in a department store at night.  Later, my father was a radio dispatcher for a trucking company.  When he realized that he couldn't really make a good living in Northern California, he moved to Southern California and drove trucks and eventually worked in the oil fields.  First my brother Jack was born, and then yours truly.  Dad worked even harder to provide for his family.

In the early 1960s, when my father was about 30 years old, he joined the Long Beach Fire Department.  There,  he found his niche.  These are my strongest memories of him. When I was a boy and a teenager, this is how I remember my father.

My father worked very hard at his job.  My father is not at all political (well, neither am I!), but continued to advance via hard work and excellence.  Eventually, he became a Captain of the LBFD, and finally a Battalion Chief.  During the run up to becoming a chief, my father finally earned his Bachelor's degree from Cal State Long Beach in his 50s (which still impresses the heck out of me).  After retirement, he worked for many years teaching Fire Science at local colleges, to help men and women prepare for careers in firefighting.  As I have mentioned, there is something of the military in my father, and he blossomed under the organized environment of the fire department.

Plus, he genuinely made a difference.  I mean, I enjoy teaching and doing research.  But I have no illusions about my job:  I save no lives.  My father---personally---has saved dozens of lives and delivered many babies during emergency situations.  Every day, he made the world better in concrete ways that can be listed and applauded.  So I respect him not just as my father, but as someone who is truly a hero.  And why not?  Firefighters run into burning buildings to save other people.  Can you think of a better definition of "bravery" and "hero"?  I can't. 

My father tries to present himself as an "aw shucks" simple man, but he is very intelligent, thoughtful, and introspective.  He despised people receiving special privilege, hated prejudice (despite his salty and non-PC language), and generally stood up for fairness.  When women first began to become firefighters (we used to call people in the profession "firemen"!), my father was at first troubled, growing up where and when he was. Yet when he met young women willing to work hard, and devote themselves to the goal of becoming a firefighter, who were honest and honorable, my father became a big supporter of women in that a time when that point of view was not common.  

A most unusual man, though he would say something rude in response to that complement, I'm sure.

My father has an unusual sense of humor.  Yes, he loves to tease, and I learned quickly to not take the bait.  I well remember playing the card game "Uno" with my parents on one occasion.  My father kept "saving up" cards that would force me to draw more cards from the deck, passing up opportunities to use them strategically.

"Dad," I finally said, "why are you doing this?  You keep burying me in cards and Mom wins every game."

"You don't understand," he replied with a grin, moving an ever-present toothpick from one side of his mouth to the other.  "I don't care who wins as long as you lose."  And my father would grin his faux-evil grin at me.  

Yes, it was about the teasing, but the teasing was a form of affection.  He never did that kind of thing to people he didn't know or didn't like.

There is a lot to say about my father, because he was and is a very complex and interesting man.  To my father, being honorable and honest were the cornerstones of life.  He might try to cheat me a bit at cribbage, but he was as honest as a Roman judge otherwise.  Very, very high standards.  And a burning hatred for unfairness.  My father had seen much unfairness in his life, and insisted on fairness in his own sphere of influence.  I feel much the same way, in my little laboratory and in my classroom.

My father loves little kids, and always has.  Teenagers are a different story, yet he was fair and honest with me.  Remember, this is a tough man who had little, who worked at least two jobs while I was growing up, and was tired all of the time.  Dealing with "Emo" children such as myself who didn't like sports and were not "tough" was probably not his favorite pasttime.  Yet I forgot that, as a Captain on the LBFD (while I was a teenager), my father had a great deal of experience dealing with young men not a whole lot older than yours truly.

Once, when I was sixteen, I had had my adolescent heart broken by a young lady.  Dieseling on testosterone fumes, I asked my father for advice.  My brother was in college, and my mother visiting her own mother in Northern California.  Dad sat down, lit up one of his menthol cigarettes (which he smoked because no one would steal any from him at the fire station), and asked me to explain the situation.  So I did, in all my Emo glory.

My father considered the situation.  Took a draw on his cigarette.  Blew out the smoke like a dragon, and observed "Jeez, kid, you got a lot of free time."

At first, I was angry that he didn't honor my existential despair.  But the truth was different.  My father explained to me that we all have limited time on this planet, and got to choose how to spend that time.  Did I really want to spend a whole lot of time on that particular issue?  Then he laughed at me and clapped me on the shoulder.

My father is kind of an Eric Hoffer type:  a working class type of  philosopher.  Seriously, Hoffer wrote things that my father often said (and Hoffer is well worth your time, incidentally).

Later on, when I attended UCLA, I had some trouble in my classes.  For the first time in my life, I earned some bad grades.  Part of that was due (again) to my dieseling on testosterone fumes, and being too proud to ask for help (after all, I did pretty well in high school).  This was before the FERPA laws, so that the postcards with my college grades would arrive home for parental review each quarter.

Times have changed.

So my second quarter grades arrived that winter, and they were, um, decidedly not stellar.  My mother, rest her soul, let me have it with both barrels.  I dreaded my tired, overworked father getting home from the fire station after a 72 hour shift and giving me the business, only more so.

I will never forget sitting at the small table in our kitchen on Poinsettia street in Long Beach, California that day.  My father, toothpick in mouth, tapping the postcards on the table top.  

"Is this the best you can do?" he asked evenly.

I started to defend myself, to explain myself.  Working up some righteous indignation, since no one could possibly understand my life and challenges.  Forestalling all of this, my father held up his other hand.

"If this is the best job you can do, son," he told me, "then I am proud of you.  No one, and I mean no one, can ask for more than your best."  He paused, and tapped the postcards again on the tabletop.

"So one more time," he asked, his green eyes on mine, "is this the best you can do?"

I mumbled a bit, and allowed that I could have done better.

"Very good," my father replied.  "Now, how can I help you to do better?"

He found out about one of the jobs I had taken on campus, because I felt badly asking for spending money.  My father worked out a deal with me. He would give me a little money under the table, and I would quit the extra job, and study more.  

Bit by bit, my grades improved, though not like the grades my much smarter brother earned.  I had to sweat it more, and that is okay.  My mother would point this out (I miss you, Mom, but it is true).  Dad never did.  Not once.

As a senior in college, I was amazed to learn that I had gotten into PhD programs all over the country (my brother had talked me into applying to places I would normally not have considered possible).  My grades were good in my Biology major, but overall quite pedestrian.  I had done very well indeed on the GRE.  And I surely did love research.  I guess some admissions committees saw my potential.  So I was so happy to share with my father all these acceptances.

My father almost never cries.  But there were tears in his eyes when he said, "Son, I am so very proud of you.  But I am ashamed to tell you that I just can't afford to send you to places like Yale or Stanford.  It's a big honor, but I just can't do it."  I could see how much that cost him to say.  Pride is expensive, but my father worked so very hard, and pride in what he had created for his family was reasonable.  

I explained to him that each letter referred to a stipend that would pay my way (modestly).  At Yale and Stanford, there were NIH training grants, for example, that would pay my tuition, fees, and provide a (very small) living stipend.  My father couldn't get his brain wrapped around that concept; when my brother went to law school, the idea of loans made sense....despite what my offer letters explained.  In fact, when my father drove up to Palo Alto with me to start my graduate career, his last words before he drove off were "If they screw you over, kid, call me collect and I'll get right up here."

And that's the point about my father.  The life I chose made no sense to him at all...yet he did his best to help me out.  I wasn't as hard of a worker.  I wasn't athletic.  I wasn't tough.  But what I was, was my father's youngest son.  That counts for much more than a father who did understand academia, I think.

I could tell my going to graduate school and earning a PhD was a big deal to my father.  He even got me---one of the few "surprise" gifts I have ever received---a graduate school class ring!  He bought an old book, hollowed it out, and hid the ring inside.  I wear it in his honor.

As my father grew older, and retired, and helped my mother with her long struggle with cancer, I think that I learned to appreciate and understand my father better with each passing year.  What most people do not understand about my father (and it is true for my brother and I both) is that he likes to make people laugh, but is in fact a very serious person...and not particularly upbeat.

But we do like to make other people laugh! 

Here is my father with one of the few genuine smiles I have seen on his face, except when he is hugging his grandchildren.

That is not quite the faux-evil grin, but similar.  He is a character, my father.  My goal, growing up, was to make him laugh.  From time to time, I was successful.    

My father is from a generation that was decidedly not "touchy-feely."  Thus, there were many things I could not comfortably discuss with him.  Yet, we bonded over my becoming a father.  I was late to the fatherhood game, having my sons at 42 and 45.  When I called my father with news of my first son Anson's birth, my father said "Kid, now you have the tough job:  you have to be his father, not his friend."

It took me a while to realize that he wasn't talking about me being a father, at all.

Years later, I was standing in front of my parent's house in Mission Viejo, California, chatting with my father.  Down the street, I saw a man cross the street with two little children, heading to the local park.  

My father pointed at the distant figures with his cigarette.  "That fellow," he told me, "got laid off six months ago.  His wife went back to work, and he looks after the kids."  After a couple of puffs, he said "What must the kids think?"

Without thinking myself, I replied "That their father is taking them to the park."

It took me a while to realize I wasn't talking about the people down the street, either.

To my father, work was everything.  And because he worked so hard, he missed a great deal of his sons growing up...and knew it.  But he had to provide for his family.  That was Job #1.  

In 2005, when my sons were small, my wife and I moved to Tacoma, Washington.  And from that distance, my father got to see my children growing more quickly than I did, since I was there every day.  For example, here are Anson and Zachary the day before we moved to Tacoma:

And here they are on Friday, the last day of 7th grade for Anson, and the last day of 4th grade for Zachary:

There is a saying I like:  Time doesn't fly, it flees.

In every conversation with my father, he has emphasized being a good father, the best father possible.  He always cautions me that no one is perfect, but to do my best.  Even as my mother became very ill, and finally passed away.  And afterwards.  In each conversation I have with my father, he discusses how to be a good father with me, the ups and downs, the challenges and the successes.  I treasure those conversations.  I never thought I could have had those conversations with him, growing up.  

It was very sad to lose my mother, of course, and I have written about it before.  But I am glad that I talk with my father frequently, and that he came up to see us last Thanksgiving.  Here is a shot of he and I (with my hambone youngest son photo-bombing us in the back).

And here he is with my sons.  That is probably the most genuine smile I have ever seen from him.

Starting in January, my father has been fighting respiratory diseases.  He has been hospitalized twice, and has good days and bad days.  Our goal is to get him home, as soon as he can take care of himself (with some folks to help out with physical therapy and such).  

Hospitals are not fun for patients.  My uncle arranged for my father to have an iPad, and my brother's son Justin Martin has been teaching my father how to use it.  I hope that will help my father feel more connected.  Here he is today, enjoying some, um, non-hospital approved food (well, Carl's Junior is pretty good).

He is tired, and on the mend, but that's my Dad!

So, Dad, let me take this opportunity to say "thank you" for providing me with a home, for honoring my education (and helping out a lot), for standing by me through thick and through thin.  I would like to be 50% of the father you have been to me, to my own sons.  Whenever I feel stressed, I remember what you dealt with, and successfully.  Salute!

I read a lot of science fiction.  There is a great novella, written by Steven Popkes, called "The Egg."  In this story, a little boy is looked after by a strange alien creature called Gray.  Gray teaches the little boy important lessons, and none so important as what the alien calls "the three loves."

To Gray the alien nanny, the three loves are "Love of family, love of work, and love of duty...and always, always in that order."

My father would say much the same.

Happy Fathers' Day, Dad!  I can't wait until you get home from the hospital, so we can play some cribbage.  My family up here in Tacoma loves you, and most especially so do I.