Tuesday, February 25, 2014

A Nice Suprise---One of My You Tube Videos Is On Boing Boing (Plus An Update!)!

As the Polar Vortex begins to grip part of our country again this week, I was thinking about how in Tacoma we have not had a great deal of super cold weather this year.  Lucky us.

We microbiologists use "the cold" a lot in our work, from keeping enzymes chilled, to making cryogenic frozen stocks, and similar activities.  My -80 degree freezer is always humming in my little research laboratory.

Imagine my surprise when someone on Twitter alerted me to the fact that one of my YouTube videos is on the "cool tech" website Boing Boing.  Here is the link.  And here is my video, again.

video


The author of the post, Maggie Koerth-Baker, did a great job of explaining the fascinating ice nucleation bacteria.  I do indeed use Pseudomonas syringae as my "ice-nucleator" in a demonstration to my Microbiology students each year, and I wrote about doing so on this blog two years ago here.  Though the video in the Boing Boing article is fine (that is my hand in the video, by the way), I like this next one better, since it has bonus student commentary---and you can see the nucleation event pretty clearly.



I had heard about ice nucleation bacteria for many years, but learned the "demonstration" from the great Jo Handelsman and her colleagues, who use it as a classroom exercise with introductory students.  So my hat is off, once again, to Jo and company.  Joseph Conrad in "Lord Jim" wisely wrote that "You shall judge of a man by his foes as well as by his friends."  On the basis of my friends, I am lucky and rich indeed!

This incident also shows the value of Twitter.  I literally had no idea that someone was writing that article, and the only way I found out was being alerted by a "microtweep."

Anyway, thanks to Boing Boing and Maggie Koerth-Baker!

UPDATE:  I am very grateful to Ms. Koerth-Baker, again, for her writing about that YouTube video of mine.  The video has appeared in several other places besides Boing Boing.  

The video (and short write up) have appeared on Gizmodo in Australia,  the Periscope Post in Turkey, the Business Insider in India, Digital Journal, and most surprisingly to me,  the Huffington Post in the United Kingdom. Interestingly, not a single one of these news organizations dropped me a line or informed me.  No harm was done, nor was I misrepresented. But as I mentioned above, the only way I heard about this was via people reading the material letting me know! I'm glad they did.

I was also contacted by the folks from the PBS show Radiolab. When I spoke with their representative, I was surprised to learn that they had not read or seen any of the news reports or videos discussed in this post! The story they told was that they had become interested in rapid ice formation via bacteria (snow making, maybe?) and asked around.  Someone at Princeton University (I don't know who), gave them my name.  

I do not know if I will actually have a real interview to be broadcast (I don't think it likely, to be honest), but it was a LOT of fun for me to talk with them about science education, bacteria, and related topics.

Coincidences abound!

The other amusing part was that the YouTube video that Boing Boing popularized (the first one in this post) has had more than 60,000 views now...and it had had less than 2,000 just a few days ago.  So the "Social Media Sphere" (maybe noosphere is a good expression, with apologies to Teilhard de Chardin) is a powerful entity.  Anyway, more than a few people have criticized my video, claiming that it was rigged, or had nothing to do with bacteria, or (my favorite) was carried out using a sodium acetate solution (which also can precipitate from a seed impressively).

These nay sayers did not read about bacterial ice nucleation in the lab or the classroom (referenced and linked above).  And they also give me a great deal of credit for being far brighter and more devious than the sad reality suggests!

Thanks for the interest and for reading.  It will be interesting to see what happens next...

UPDATE #2:

NPR's show RadioLab did indeed have a segment discussing ice nucleation effects, including from bacteria, here.  Sadly, I was not an on-air interviewee.  A couple of staff members talked with me and communicated via e-mail with me about the topic, and I was happy to help out.  And I did get a acknowledgement.  They even mentioned my video without using my name (oh, well).  

On their website (linked above), the NPR folks did create a video showing ice nucleation (and a toy horse---listen to the podcast to understand the interesting reason why).  Here is the video:


Cool (!) as it was,  I have to say that I like my videos better (a proud "parent" perhaps?).  And the second video I posted shows the initial nucleation event very clearly---with, as I say, bonus student enthusiasm!

Someday I will get to promote Microbial Pride via radio or television.  Though I will sheepishly admit that I have a perfect face for radio...

Wednesday, February 19, 2014

On a Cellular Level, All of My Freshmen Biology Students Are Overachievers!

In my freshman biology course (Biology 111, "The Unity of Life"), we cover a number of diverse topics in cell and molecular biology as we race along in lecture. Historically, students love the genetics section and have reservations about biochemistry and metabolism related topics.  Though I am trained as a microbial geneticist, I cannot think of a more central topic in biology than metabolism---after all, it is how the very machineries of life grind along, day after day.

I remember a cartoon on the Internet, years ago, showing the cartoon character Homer Simpson, snoring away on a hammock, with a beer can balanced on his ample belly.  The caption was "On a Cellular Level, I'm Pretty Busy."  Because it is true.  

Even while a student's attention might wander, the machinery of her or his cells are ticking along at impressive speeds.  DNA is replicating, unwinding at hundreds of thousands of RPM (without generating heat!).  Proteins are being synthesized and recycled. The endomembrane system is a complicated traffic snarl/ballet of vesicles carrying cargo to diverse destinations within the cell. 

One of the great things about Twitter is the ability to communicate with different people from all over the world.  Thus, I was able to get to know the great "Beatrice the Biologist," who does wonderful science-themed cartoons.  You should definitely check out her website here.  She wrote and illustrated a wonderful children's book about cells ("Amoeba Hugs and Other Nonsense") and recently released a truly great book for students and adults about genetics ("What's In Your Genes?").  

I told "Beatrice" about my class, and the challenges of telling my students about the intricate, active, and interrelated metabolic processes that exist in each and every one of their cells .  I then commissioned a comic from her on this topic.  Here is what she created.

Pretty much nails the concept, right?

"Beatrice" wrote about this cartoon here (again, her blog and website are very much worth your time).  

So I guess it really doesn't matter if a student is eager and overengaged, overwhelmed by new information, or not even in lecture that day. Because on a cellular level, each and every one of my students is indeed an overachiever!

Thank you, "Beatrice"!

My class thanks you, too.



Today is a good day, even with a pile of grading.

Friday, February 14, 2014

A Bioluminescent Valentine's Day!

I was pleased and flattered that the wise and elegant Moselio Schaechter, of the American Society for Microbiology sponsored "Small Things Considered," listed this blog as favored reading recentlyElio, if you are reading this, I continue to be amazed at how well you keep up with the dizzing pace of Matters Microbial™; I think you remain one of my Microbial Heroes™, as Jon Eisen describes them!

Elios's kind words reminded me that I should post more frequently, since some people are reading my essays! 

Even though many of my colleagues at large educational institutions have much larger classes than I do, my current freshman "Unity of Life" course has 48 students (all of them in lecture three days a week, and three lab sections of 16 each during the week) and certainly keeps me jumping. The students come from a wide variety of backgrounds, ranging from business to exercise science to psychology to biology.  It is thus a moving target pedagogically,  especially as I move into the more challenging areas of biochemistry and metabolism. 

However, I cannot let today's holiday pass unnoticed.  To be sure, I am a microbiologist and geneticist, but a romantic heart beats inside me just the same. Thus, I would like to share with you some of my "bioluminescent art" for Valentine's Day!  As described from time to time on this blog, I grew up cultures of Photobacterium leignothi and "wrote" onto Petri dishes containing appropriate nutrient medium.  I then incubated for a few hours, and voilá!

One the central concepts I discuss with students in all of my classes is how microbes communicate with one another using low molecular weight molecules. This chemical "language" can control gene expression, allowing some genes to only be activated at high population densities.   This process has come to be called "quorum sensing," and it is a very hot topic indeed in microbiology, controlling such diverse processes in many microbes as pathogenesis, pigment production, adhesion, and of course bioluminescence.

Since quorum sensing is a critical topic in biology, why not immortalize it on Valentine's Day, with bacteria using this very process to generate beautiful light in the darkness?  Here is one such image.


Another image image with the same theme.


In this photograph,  I am trying to get more reflection from the shelf on which the plates are propped.


And finally, I need to recognize the many roles my wife of 15 years, Dr. Jennifer J. Quinn, has played and continues to play in my life.  Jenny has exemplified loyalty, honor, professionalism, and love in ways that humble me daily.  I cannot imagine life without her.  Jenny brings light into my life so often, and I would like to commemorate that fact in bioluminescence here.


I hope that everyone reading this has a lovely, lovely Valentine's Day.  And considering how frequently microbes engage in horizontal gene transfer, I would like to wish your mutualistic and co-evolved diverse population of microbiota a romantic day as well!

Saturday, February 1, 2014

Freshman Biology, Word Clouds, and Preconceived Notions

According to my teaching schedule here at the University of Puget Sound, Spring Semester is when I teach my "freshmen level" Biology 111 course.  Biology 111 is nicknamed "The Unity of Life," and that is the way I teach it:  just like Jacques Monod wrote, what is true for elephants is often true for E. coli.  Well, up to a point.  I do think it is important to remind students of the common strategies used by life on Earth, so the course title makes sense.

A couple of characteristics of the course stand as challenges to be overcome.  First, the class is large for a small liberal arts institution---48 students in lecture three days a week, split up into three lab sections of 16 that meet once a week (apologies to my colleagues at large institutions, but do keep in mind that I teach lecture and all the labs).  Anyway, the students get a fairly substantial dose of flamboyant Doc Martin, even though it is a "large" class. Here they are on the first day of class last week.  Fingers crossed that it is a fun class; so far so good.



The other challenge, of course, would be dealing with and overcoming the differing levels of preparation for this course.  We not only get folks interested in majoring in Biology, but also Psychology, Exercise Science, and even Business.  Some folks haven't had any chemistry at all since early high school, while others are quite savant on the latest in biology and biochemistry. Folks interested in, for example, human-centric biology may become frustrated by discussion of Matters Molecular™.  So I work hard to make things relevant to all the students, no matter the background, using everyday examples (the concept of structure and function in light of sugar substitutes is one topic I cover). It's definitely a moving target.  So I need to have a "snapshot" of how the new students perceive aspects of biology.

How best to evaluate "where" the students "are" coming into my classroom?  Why not use "word clouds"?  Word clouds are ways of representing "single word" answers to questions in a fairly artistic fashion, with the size of the word often representing its frequency. 

On the second day of class, I said the word "germ" and asked the students to write down the first single word that popped into their heads.  Here are the results.



The first thing that leaps out at me from the response is how people conflate "germ" with "bacteria."  Fair enough, if not complete in a definitional sense.  But notice all the negative terms involving disease, "dirtiness," and the like.  My favorite from this word cloud would be "phobia" or "germophobe," because certainly people seem to have an anti-microbe phobia these days!

The term "germ" was popularized originally by Louis Pasteur.  But he didn't mean anything relating to disease with the word.  The original intent came up as part of his campaign against the concept of spontaneous generation. A "germ" meant "a bit of life," and with those lovely goose-necked flasks (and I admit I would like to own a replica!), Pasteur was able to convince people that life always came from life!  Unfortunately, the term "germ" is "meme-locked" as meaning something associated with disease.  I have vowed to change that.  Pathogens are like the juvenile delinquents of the microbial world:  small in number but they get ALL the press!

I then said the word "bacteria" and asked the knee-jerk one word response from the class.  Here is the word cloud that generated.



Again, notice the conflation of "bacteria" with "disease."  Sigh.  I have some work to do, as do secondary educators!  But amidst all the "dirt," "infection," and "gross" type responses, I had some interesting ones.  "Interesting" made me feel good.  "Tiny" is not always true, but is reasonable.  Some positive responses appeared:  "good," "probiotics," "yogurt," "cheese," and "antibiotics." There were also some odd ones:  "claw" I have no explanation for, nor "mistaken."  "virus" needs some clearing up, as does the seemingly popular "mold" (since bacteria are not fungi!). 

It certainly gives me a great deal to think about in my introductory course, and hopefully some insights for middle and high school teachers.

I then moved on and asked the first "single word" response that appeared in their cerebral cortexes when I said the word "cell."



Well, it is good that "biology" came first (again, size of the word is related to the number of times it is seen in the responses).  But look at the other words:  "complicated," "cancer," "life", "small," and so forth.  Lots of comments refer to parts of cells, complexity, size, and so forth.  I cannot explain "goku," as I certainly hope that Dragonball is not part of cell biology!  Finally, some people thought of "cell" in a different context by writing "inmate" and "prison."  But I think we can agree that more people have appropriate thought-images of the word "cell" in their brains.

And finally, the same exercise when I said the word "DNA" to the class.  Now, it may well be that the best way to do this is not ALL on the same day! Regardless, here is their response.



I found this to be VERY interesting, indeed.  What conclusions can we draw from this last word/concept cloud?

Well, "genetics" or "genes" appear to be the #1 answers, and this shows how the term "DNA" has been perceived in everyday life, I think. 
Most everyone else had a nearly equal spread of different terms, clearly originating from different sources. 

Some students were keyed to procedural words like "PCR," "data," and "forensics."  A few students showed their enthusiasm with "awesome" and "cool." Others referred to structural words, such as "ladder," "spiral," "acid," "sequence," "doublehelix" (not really one word, but okay), "sugar," and "strand."  Still other students opted for concept driven response-words, like "evolution," "unity," "code," and the like.  "Watson" showed up, but no Crick, Franklin, or Wilkins (I will fix that).  

There were some unusual choices, as well, since as "red" and "blah."  Blah?  Well, it is a response.

At the risk of sounding like a social scientist, the names that we give ideas and concepts can alter the way in which we think about those ideas and concepts.  So the "knee-jerk" responses to words can give a useful snapshot depicting HOW certain ideas are perceived by a classroom.  This in turn can impact our own teaching in response, to improve student learning and outcomes.

Why not give wordcloud-responses a try in your own classroom? In addition, thinking about this might give students some perspective into how they encounter and assimilate new ideas.

Let me know what you find out!