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.

Friday, May 8, 2015

Freshman Biology, Creativity, and Extra Credit...

Sigh. Still behind on blogging. Yet there are some good (and some not-so-good) things worth sharing.  So let's start with the good!

For my normal teaching schedule, I have six instructional units per year. That breaks down in the following fashion.  In the Fall semester, I teach my junior/senior level Microbiology course with two laboratory sections (And this year I am going to push for a more appropriate name in my department: "Microbial Diversity." Wish me luck!), along with my Freshman Writing Seminar ("Never Really Alone:  Symbiosis and Parasitism Around and Within Us."). In the Spring semester, I teach a large (48 students) introductory cell and molecular biology course (Biology 111: "The Unity of Life"), with three laboratory sections.

I am not complaining, but yes, the schedule has me jumping (since I also work with four research students during the academic year, as well).

As readers of this blog know, I enjoy allowing students to explore their creative sides in my classes.  Not only are the results in turns impressive, amusing, and surprising, but I continue to insist that this approach is pedagogically sound.  For one thing, students invested in their own projects work harder, and usually learn more than they had expected.

I have done this for the past several years, and enjoyed some remarkable successes from students, some of whom were quiet and withdrawn in class. There are many learning strategies, and one size decidedly does not fit all.

Let me show you some of the wonderful things that my (mostly) freshman #Bio111A students did for this assignment during the current semester!  Many of these students are nonscience majors, incidentally, taking the course for breadth requirements!

Lexie created quite an interesting (and large canvas) exploring her interest in nondisjunction and fetal development.



It's a "Doc Martin Truism™" that I love all Matters Microbial™, and my students always hear a great deal about this kind of thing. I do try to ramp it back, my some of my monomicromania still comes through.  Thus, Danielle and Alexa share "It's Raining Microbes" with you.


Please keep in mind I have tried to shame my seniors for over ten years into making such a parody video.  It took two freshmen (Voice and Business majors) to do it for me.  Thank you, from the bottom of my microbial heart.

Andrea combined her love of The Beatles with internal cellular geography, as you can see here from the cover of her mini-book!


Eden decided to explore central metabolism by creating a game, as you can see here.  She tells me she learned a LOT by making this project, and I can see why.  Brilliant and challenging.


I have always enjoyed stop motion photography, and Taylor did that idea proudly in her exploration of mitosis---on a cake, no less!


Gabby created several pieces of art, including this view of the architecture of a cell.  Nice!


Some students are utterly fearless in their videography.  Check out Anna (ANNAphase) and Crystal (Crystal Chiasma) giving a new spin to "Hey Ya!" by Outcast as "Hey Cells!"


Nico and Selene created a "children's book" explaining how glucose is broken down in a cell---"The Tragic Tale of Gluci."


Lauren decided to mix her mad baking skillz by creating a group of cookies that represent a cell and all of its contents.  Personally, I preferred the nucleolus:  tasty and informative.


Anna, Nate, and Tyson decided to re-write "Happy" as "Cell Cycle," and I was impressed by the very quiet Anna's vocal skills. Aren't you?


Andrew, quiet and good natured, told me that he wanted to "sculpt" a three dimensional view of a cell, mitochondrion, and chloroplast. It's not easy, and I think he did a good job!


Lauren decided to depict meiosis in stop motion, and did so in an entertaining fashion.


Most students are fascinated and worried regarding cancer cells when I discuss that process in class, and Maggie was no exception. She created this fine artwork depicting such rogue cells.



Each semester, I get various surprises from the quieter students. Who knew that my student Jack made "techno" music?  So I introduced him to various websites and articles about turning DNA sequences into music.  Jack focused on the VNTR repeats present in different copy numbers with the human locus D1S80.  Here is his creation.


Isabelle and Jule, possessors of always unusual and humorous views,  created a "model house" in which the different items found there are recast as parts of a cell.  My favorite part?  A drawing of a housecat was labeled "lysosome."  Ha! 



Now, most of my students know that I adore bioluminescence. And who doesn't?  With that in mind, Claire, Mickela, Caroline, and Maria created an a capella view of bioluminescence in "Let It Glow!"


Kristina is a lover of classic rock, so she decided to depict the various stages of mitosis in the style of Led Zeppelin album covers. Wow! What would Jimmy Page say?



Jayce created a lovely composition regarding the Master Guardian Protein of the Cell, p53, as his "Genome Hero," complete with ukelele and beatboxing. 


Tori decided to illustrate issues involving nondisjunction and meiosis via stitchery on pillows---here is an example of one of Tori's quite detailed creations.



Speaking of fearless, Zoe decided to perform in voice and dance "The Cycle of Krebs" to the tune of "The Circle of Life" from "The Lion King." 


McKinley did something unique and appropriate:  she created a "light portrait" of the Z diagram of photosynthesis! Illuminating!


Sam and Lydia created a "Bloodline News Report," complete with commercials for various products.  There are lots of "in" jokes from class here.  Apparently they listen to my silly jokes as well as the material!


James and Adrian decided to create a video illustrating the electron transport chain from their perspective, as you can see below. What was most amusing to me was their attempt to involved the Red Headed Stranger, Willie Nelson, in their efforts (I would have given cash money to hear his actual response).


Finally, there were several folks who either asked that their projects not be depicted on this blog, or created items that don't translate well to the visual.  Hats off to them regardless---their work was impressive and valuable to me as an educator, and I hope to them, as well.

Savannah created a card game relating the parts of a hospital to the parts of a cell, with instructions.

Bonnie created a group of models cosmetically recreating the effects of several viral disease (a Viral Catwalk?).

Lindsey made bread, and wrote up a nice discussion of how the process related to several critical concepts in class (in particular fermentation as well as other aspects of glucose metabolism).

Liam tried to make "fancy pancakes" to show the various stages of mitosis. It was a bit tricky, but delicious regardless.

So, readers.  As you can see, my students here in Tacoma are brilliant in so many different ways.  Educators, give this approach a try.  The students had fun and (ssshhhh) learned a great deal doing so.

So did I.

This, right here, is what makes my job so worthwhile.  

Sunday, February 15, 2015

Happy Microbial Valentines Day---In Words of Living Light!

Well, time is flying, yet again!  I am beginning to get a better handle on my time, but still feel like I am swimming upstream.

But blog posts are not going to happen unless I...um...write and post them.  There is a great deal that is going on for me professionally that I hope to announce soon, but in the meantime, here is a short post.

Valentines Day is fun for many people.  I certainly have enjoyed it a great deal over the years.  So why not mix it up with microbiology?

Most people who know me (or read this blog) are aware that I enjoy "painting" or "writing" with bioluminescent bacteria.  I then photograph the results in the dark.  For example, here is such an illustration featuring my undergraduate laboratory students.


I usually "paint" or "write" with Photobacterium leignothi, a bacterial strain originally isolated from Kaneoh'e Bay in Hawai'i by my friends and colleagues Eric Stabb and Ned Ruby.  It's very bright indeed, and perfect for this purpose.

So with that in mind, why NOT a "Living Valentines Day" card for my lovely and brilliant bride Dr. Jennifer J. Quinn of the University of Washington - Tacoma?



I even wrote a little Valentines Day poetry for her in living light.



But I also wanted to give a bioluminescent "shout out" to all of my microbiologist friends and colleagues.  So...



The entire process of light production by marine bacteria follows the density dependent process of quorum sensing (a concept that my poor students hear about endlessly from yours truly).  In any event, it occurred to me that the basic concepts of quorum sensing were worked out in luminous marine bacteria.  So why not write a "microbial haiku" about quorum sensing, appropriately illuminated by bioluminescence?


It's actually fairly challenging to write many words on Petri dishes with swabs (my normal way of carrying out this kind of task).   So I again tried a "Burma Shave" approach,  trying to write with toothpicks below.  It's not as even as I would like, but is another strategy.



Next time, sterile fine paint brushes?  If this keeps up, I will have to learn to paint as my wife does! 

In the meantime, I hope that everyone had a fabulous---even glowing---Valentines Day!


Wednesday, December 31, 2014

Do You Need Inspiration For 2015? Consider Randy Pausch's Advice.

Time does indeed move so very fast with every passing year.  We are coming up on 2015 as I write this post. When I was a boy, the year 2000 was a strange and exotic destination---I would be middle aged, and the world would be so very different.  Bright and shiny.  I thought we would have personal jet packs and spaceships to Mars. Oh well.  

At the same time, there are wonders all around us, if we but take the time to look and listen. Quiet contemplation is something from which we could all benefit, but we seem to have too little time for it, as a culture.

The approach of New Year's Day makes most people reflect a bit. And I was doing so, as the narcissist (and not in the self-congratulatory sense of the term) I suspect I am. I spent some time feeling unhappy with the things I had not done, the progress not met, the potential not met, the accomplishments not realized.  I felt and feel more than a little bitter at not reaching the dreams and goals in my heart. 

While it is true I am the luckiest person in the world from my perspective (to have the wife and children I do, the moderate health I enjoy, and a job that meets many of my professional needs), there is something in all of us that dreams of, as Edward G. Robinson put it in the move "Key Largo," more.



Then I remembered a hero of mine,  Randy Pausch.  The late Dr. Pausch was a charismatic computer scientist who chronicled his battle with pancreatic cancer and become something of a media icon before his death in 2008.  Pausch wrote a book called "The Last Lecture," which is both practical and highly inspirational. I have given away dozens of copies to undergraduate students.  If you have not read it, you should.  ASAP.

There are several quotes from Dr. Pausch's book that stick with me. I would like to share them with you.

This first one is so very important, especially to how I view science.
When you're eight or nine years old and you look at the TV set and men are landing on the moon---anything is possible.  And that is something we need to not lose sight of, is that inspiration and permission to dream is immense...it's important to have specific dreams.
I was that young boy watching Neil Armstrong on grainy television in 1969.  And many people, and many students, seem to be about settling, about limitations.  Focusing on what cannot be done, instead of working to...well, make their dreams come true.

Which leads me to:
Never lose the child-like wonder.  It's just too important. It's what drives us.
I have always loved science, even when it does not love me back. And I am awestruck by what is being discovered nearly every day. It's what makes me a scientist, even at my level.

Staying upbeat can be a challenge.  Dr. Pausch has it spot-on.
You just have to decide whether you are a Tigger or an Eeyore. You have to be clear where you stand on the Tigger/Eeyore debate.
I have spent too long as an Eeyore, when I am temperamentally meant to be a Tigger.  How about you?

Some wonderful advice about education.
The best way to teach somebody is to have think they are learning something else.  I've done it my whole career. And the head fake here is that they are learning to program, but they just think they are making movies and video games.
I have done that with my "extra credit creative projects" in my classes in recent years.  Pausch is absolutely right.

That in turn led me to:
The best gift an educator can give is to get someone to be self-reflective.
Yes! I have long said that the three most important words in science are "I don't know." Some folks don't agree, but I don't care. We can fix the "I don't know," and history has shown that inflexible and self assured attitudes harm science more than help it.  Certitude and authority are the enemies of science. It's how we know, as much as what we know.  Science is a process, not a destination.

And, more than a little painfully, Pausch shares some thoughts about succeeding in life (and academia).
General Advice:  (i) never break a promise, but renegotiate them if need be.  (ii)  If you haven't got time to do it right, you don't have time to do it wrong.  (iii) Recognize that most things are pass/fail.  (iv) Feedback loops:  ask in confidence.
Number three is particularly important.  We really do tend to think all life is a graded exercise.

Also, some stinging truths.
Experience is what you get when you didn't get what you wanted.
I realize that many, many people have had a more challenging path through science than I have. But I have had many, many reverses, poor choices, some bad luck, and, um, not so nice people with whom to contend. It can be frustrating.  It can make a person bitter, a sentiment with which I battle often.  And Randy Pausch's spirit has long chided me with this:
The brick walls are there for a reason.  The brick walls are not there to keep us out.  The brick walls are there to give us a chance to show how badly we want something. Because the brick walls are there to stop the people who don't want it badly enough.  They're there to stop other people.
I re-read this quote a lot when I am feeling low.

Here is one with which I have always struggled, courtesy of Dr. Pausch's high school football coach:

He said, when you're screwing up and nobody's saying anything to you anymore, that means they gave up.  And that's the lesson that stuck with me my whole life.  Is that when you you see yourself doing something badly and nobody's bothering to tell you anymore, that's a very bad place to be.  Your critics are the ones telling you they still love and care.
I think that entirely depends on the critics, but there is much truth in what Pausch's football coach said.

When dealing with difficult people, Dr. Pausch is very wise indeed.
Find the best in everybody...you might have to wait a long time, sometimes years, but people will show you their good side.  Just keep waiting no matter how long it takes.  No one is all evil. Everybody has a good side.  Just keep waiting.  It will come out.
Dr. Pausch learned that from his high school football coach, again. The coach put it a bit differently.
When you are pissed off at somebody, and you're angry at them, you just haven't given them enough time.  Just give them a little more time---and they'll almost always impress you.
That one is particularly tough for me, given my path through academia, but it is also true.

Here is Pausch's quote from the end of his talk and his book that impacts me the most, emotionally:
Did you figure out the head fake? It's not about how to achieve your dreams.  It's about how to lead your life.  If you lead your life the right way, the karma will take care of itself.  The dreams will come to you. 
Did you figure out the second head fake? This talk's not for you. It's for my kids. 
Always makes me tear up. But then, I am a Sensitive New Age Guy™ in most ways.

There is much wisdom in his book.  Again, I highly recommend it.

But do read this book, and watch the videos.  You will be intellectually and ethically the richer for it, I promise.

For New Year's Day, may I suggest you watch his "last lecture"? I can promise you will find much of value in that 70-some-odd minutes.



His home page has many more resources and videos, all of which are uplifting and moving.

Let me go further, and recommend just a couple of more videos. Such a remarkable man, such a great loss. But look at how he was willing to share with all of us (and his family) quite a bit of wisdom and humor and bravery.

His widow Jai gives some thoughts about Pausch, his bravery, and the need for support into finding treatment or a cure for pancreatic cancer.



I think that Dr. Pausch's commencement speech at Carnegie-Mellon (not long before he passed away) is required viewing.



At the end of his speech, you will see Randy Pausch pick up his wife Jai to paradoxically show his strength (he was more than a bit of a showboat). She buries her face in his shoulder. I have read that she then whispered to him, "Don't you die on me" through tears, and he whispered back "I'm working on it."

Some of his dreams may seem trivial.  All of our dreams might be seen as such, from outside.  But they are our dreams.  

Randy Pausch loved "Star Trek," and had worked on some video games for that franchise.  William Shatner knew him slightly, and when he heard of Pausch's battle against pancreatic cancer, he characteristically sent a 8 x 10 head shot of himself (Mr. Shatner is nothing if not, um, self-assured).  But what Shatner wrote is moving.  "I don't believe in the no-win scenario," which is both a trope from "Star Trek," and a wonderful sentiment for Dr. Pausch.

Finally, when J.J. Abrams "re-booted" "Star Trek," he gave Randy Pausch a chance to have a bit part in the movie.  Here he is, though you need to look quickly:



So even one's most unlikely dreams can come true.

There is a poem I am fond of, by Delmore Schwartz, titled "Calmly We Walk Through This April's Day."  It has a line that always made me sad:
"...Time is the fire in which we burn..."
I first learned about this poem, in all places, from a "Star Trek" movie:  "Star Trek Generations."  It was uttered by a character trying to beat mortality in an unusual fashion (Malcolm McDowell is a remarkable actor, by the way). 

But the poem is much better than that.  The link above will take you to entire text, which is decidedly worth your time.

Notice the line I hope we can all (me emphatically included) recall more than the one that made me sad:
"...Time is the school in which we learn...."
Grab life as Randy Pausch suggested.  Make your dreams come true.  And as both Dr. Pausch and Winston Churchill urged:  never give up.

When my mother Wanda Martin was first diagnosed with ovarian cancer, I bought her this as a paperweight.



My father gave it to me the day after she passed away.  I look at it every day, and we should all take the lesson to heart.

What are your childhood dreams?  And what are you doing in 2015 to make them happen?

May 2015 make your dreams come true.  As for me, I have work to do.

Happy New Year to all!

Tuesday, December 23, 2014

Merry Luxmas and Happy Microbial Holidays!

That was a busy semester!  As the saying goes, "time doesn't fly; it flees!"  Teaching my beloved microbiology here at the University of Puget Sound, as well as a freshman writing seminar on symbioses, kept me far too busy.  I will be posting on both of these classes, which were utterly fabulous and filled with OMG™(Overwhelming Microbial Goodness) and SOS™(Superb and Outstanding Symbioses), in the coming weeks.  I will also be planning on improvements to my freshman biology course "The Unity of Life" (Biology 111, or an introduction to cell and molecular biology) to be taught next semester.  Whew.

But, in the spirit of the year, I would like to wish any and all who read my too-infrequent blog posts a Merry Luxmas and Happy Microbial Holidays, as I do each year.

First, I used LB plates with 0.2% arabinose and drew a bit with E. coli DH5alpha containing the famous plasmid pGLO, as well as the red pigmented Serratia marcescens. I tried to balance a small handheld longwave UV light with background illumination. Fluorescence versus prodigiosin created a pleasing green and red theme for the holiday, I hope.  The results match the season, even if we have not more than a slight dusting of snow in Tacoma.



Of course, I adore "painting" or "drawing" with bioluminescent bacteria.  In particular, a particular strain of Photobacterium leiognathi originally isolated by Eric Stabb and Ned Ruby from Kaneohe Bay, Hawai'i, remains a solid performer.

Here are some lovely "self-portraits" of bacterial bioluminescence. I like to experiment with reflections, as well.  Regardless, I hope that these photos amuse and showcase my mania regarding True Microbial Supremacy!





My microbiology students this year even created a "Microbial Xmas Tree" powered by bacterial electricity!



Finally, no "Luxmas" celebration is complete without the video my wife Jennifer Quinn and I made a few years ago.




Happy Luxmas to all, and to each and every one of you, Merry Microbial Holidays!