Illustrating Antibiotic Action for Undergraduates!

In my freshman biology course here at the University of Puget Sound, I think long and hard about ways to show students connections between classroom material and everyday life...as well as straightforward ways to illustrate concepts that students may not find obvious.  Which brings us to today's post.

In my "Unity of Life" course, I need to cover a lot of conceptual ground, with a limited amount of time in a one semester course.  During the laboratory sessions associated with this class, the students carry out a simple transformation experiment.  Using a very simple "single colony transformation" protocol with E. coli, and the infamous (in education) pGLO plasmid, the students plate onto LB+ampicillin (ssssh...also plus L-arabinose).  Successful transformants should grow on the antibiotic containing medium, and fluoresce under ultraviolet light.  And indeed they do:  

I like the hand-held UV lamps to be found here, which are cheap and work very well.

The pGLO plasmid carries ampicillin resistance (mediated by beta-lactamase), and an interesting fusion between the arabinose operon of E. coli and green fluorescence protein (or GFP).

I reinforce to my students the facdt that the additional DNA containing genes (the plasmid), when expressed by the bacterial cell, will alter the observed phenotype.  This seems quite simple to folks with a lot of biology under their belts, but I have found that this idea and related concepts need reinforcement:  added genes, when expressed in a bacterial cell, can alter the visual phenotype.

Then I wait for four or five days.  The nice big colonies (due to transformation by pGLO) are now surrounded by small "satellite colonies," as seen here:

Yes, this is the reason that many investigators don't care for ampicillin selection in bacteria.  I usually have students pick a "large" colony and a "small" colony and restreak them on LB+ampicillin plates.  Lo and behold, the small colonies do not grow, and the large ones do.

Now comes the fun part.  The same plate you see above, illuminated by UV light:

That's right!  The large colonies fluoresce brightly under UV light, because they have pGLO in action within their cytoplasm.  The beta-lactamase made by these cells (its gene also carried by pGLO)  has been pumped out of the succesful colony, depleting and destroying the ampicillin present surrounding the transformed colony.  Thus, the satellite colonies, lacking pGLO are both ampicillin sensitive and do not glow under UV light.

This series of photographs and explanations underscore several important points:

• Only a small number of bacterial cells in this experiment have been transformed by pGLO.
• Ampicillin clearly does not kill untransformed cells.  It is in fact bacteriostatic, and not bacteriocidal.  The untransformed cells are inhibited and just sit there glumly.  Once the ampicillin in the medium is destroyed, the patient non-growing cells will begin to grow! 
• pGLO carries two genes of importance: ampicillin resistance (beta-lactamase) and GFP.  A bacterial cell receiving this plasmid will express both, and change its phenotype accordingly.

This is all quite elementary to many readers, I am very aware.  But I believe that our students need to start somewhere, and my feeling is that this part of the lab will be remembered later.  And the knowledge gained will help the students as the information (and the techniques) become more and more complicated! 

I really enjoyed tinkering with my digital camera and taking photographs for this blog entry.  Sometimes, the results are even somewhat artistic, like this one from another satellite-laden transformation plate.

Art appears in many places!

Study Guides and Student Creativity

When I teach my freshman course here at the University of Puget Sound---titled "The Unity of Life," which means the subject matter is introductory cell and molecular biology---some of my students face the need to study harder and more effectively than they ever had before coming to college.  Each year, the second exam I give, which covers biochemistry, students tend to find very challenging, and thus that exam has the lowest class average (around 69 - 70%). 

Different students have different strategies for academic success.  I know some students who define "studying" as:  looking at PowerPoint slides, television on, while listening the music, having people over to chat, and texting with other friends every few minutes.  No kidding. The amazing thing to me is that for some students, that approach works!

The word is out on what works best for the majority of students when it comes to studying.  There are many places and pundits to consult, for a student to find what works best for them.  Sometimes the news is not what you might expect (that studying in the same location does not help, for example).  I agreed with most of what was written here.   There are even some "tough love" approaches to advice for students, like the, um, very strong (and cathartic at times for educators) "Top Ten Student No Sympathy Lines."  I myself tend to shy away from the "tough talk" approach (though it can be helpful and again cathartic at times).  Being positive, I stick with the basics:  time spent studying, not just before an exam, but consistently over time; physically writing things down (I do think that there is evidence that kinesthetic learning works for some students); coming regularly to office hours; doing sample problems; and teaching concepts to other students as a study tool (as opposed to studying together, which is not always effective).

I find that student creativity really "cements" ideas and concepts into the student brain, and this should not surprise me, given the literature on learning.  Plus, if it is a strategy that the student comes up with, it would be definition fit their "learning style."

Which brings us back to the Dreaded Examination Number Two.  Before the exam, I had told students of a group of students from years before who had done poorly on a couple of exams, and were committed to really improving. They had a study session with pizza, and after eating the pizza, wrote down everything they could think of from the class.  Soon, the pizza box was like a medieval manuscript, illuminated with concepts from the course.  The students gave me the pizza box at the end of the course, which was getting a bit ripe.  So I couldn't keep it.  But my point was clear, I hoped.

After the exam, one of the students presented me with the study guide she had made for herself, which I show here:

Yes, it looks like the unusual offspring of Albert Lehninger and Peter Max.  I hope you can see the detail and dense information (and the interesting artwork).  But it was effective for that student.  And perhaps in part because of the kinesthetics of physically writing down the material!

To be sure, there is great diversity in how students engage classroom material.  I have even heard the differences called "neurodiversity." I don't know if that terminology is eye-rolling; I think that there is some truth to it, and I am not alone in thinking about the topic in that fashion.  

Don't get me wrong:  I know that this is an uphill battle.  For example, every year I have taught full time (since 1995!), I have the following exchange right after an exam:

Me, to student:  "You look very tired.  Are you all right?"

Student, yawning and jittery with caffeine:  "Yeah.  I stayed up all night studying."

Me:  "Why would you do that?"

Student, shrugging:  "I do my best work under pressure."

Me:  "Have you ever worked, well, not under pressure?"

Student, confused:  "No.  Why?"

Imagine my sad chuckle at that point.  This happens every semester, and probably has happened at every institution of higher learning since forever.

The important thing, for us as educators, is to try to help students find the strategies that work best for them.  It can be an unpleasant process of trial and error in some cases (and sometimes does not work at all),  but if I can help a few students who were struggling find their academic footing, why, that is a great feeling indeed!  Not only that, it is part of my job.  

Cool artwork such as the study guide above is just the metaphorical cherry on top.

Happy Reaping, Talmudic Questions, Zen Philosophy, and the Value of Reasoning From First Principles.

This semester, I am teaching a freshman biology course called "The Unity of Life."  It's really an introductory cell and molecular biology course that covers an awful lot of thematic ground.  Because of the large amount of information covered quickly, I sometimes becomed labeled by students as the "bad guy" with the red pen.  I really enjoy working with students, and I have never confused the quality of human being with a score on a quiz or exam.  Fairness and clarity are very important to me as a professor in the classroom.  Still, I learned a while back that some freshmen came up with a nickname for me.  That's right:  I'm the Happy Reaper™.  It made my wife laugh and she designed a T-shirt with an image she created to celebrate.  Sigh.

The "F" business makes me a little sad, but I suppose I should just embrace some aspects of it.  The students at least say I am pleasant in the classroom when I hand back graded exams (hence the "happy" part of being a Reaper, I guess).  I really do want to help students see how the new information fits together and is relevant to our everyday world.

The class I teach is a bit large for a small liberal arts institution:  I have 48 students (lecture three days a week, three lab sections of 16 students each), so it is easy for students to, um, not obtain clarity.  It's very difficult to create rapport with students under these conditions (though I know very well that friends of mine teach gigantic classes---my class is simply large for this institution).  Thus, I work hard to reinforce overarching concepts, bring up topical examples of materials presented, and I actively encourage questions from my students.

There is a saying that there is no such thing as a "dumb" question.  Fair enough.  But there are "thoughtless" or "ill-considered" questions a plenty.  You can tell, because as the student asks the question, she or he will exclaim "Oh!" and often answer the question for themselves.  It's a great moment for the student, and the class as a whole. 

There are also questions that come up in lecture or lab which are seemingly simple, yet hard to answer---and cannot be easily answered by running to Google or Wikipedia.  The great Elio Schaechter calls them "Talmudic Questions" on his fine ASM-sponsored blog relating to matters microbial, "Small Things Considered."  When I teach microbiology next Fall, I will be using many of Elio's great Talmudic Questions as "jumping off" points for student discussion and creativity.

I would like add another category of extremely useful and thought-provoking, yet seemingly simple inquiries:  Zen Questions.  I came up with the label in my classroom from reading the 1970 book "Zen Mind, Beginner's Mind" by the great Shunryu Suzuki many years ago.  It is characterized by the Zen concept of Shoshin.  Here is a wonderful quotation illustrating my point:

"In the beginner's mind there are many possibilities, but in the expert's there are few."

I have long said that the three most important words in science are "I don't know."  No, we shouldn't celebrate not knowing things, but false knowledge becomes an intellectual prison, and closes down the mind.  There is a nice essay related to this here.  "I don't know" allows you to sit back, and look at a problem with new, fresh eyes, without preconceived notions.  That is what Suzuki meant, and I contend it is an important part of science.  When I do this exercise, I often come up with new and valuable insights.

How best to illustrate this idea?  I would like to share the following story, from 1987 or so.  I had been working as a postdoctoral student in San Diego, and had fallen in intellectual love with bacterial bioluminescence.  Many microbiologists have the same fondness for blue-green light at 490 nanometers, and that affection sometimes leads to photographs like this, where I illuminate my own face with microbial light!

There are many photographs like this one, taken by microbiologists with similar interests; I am by no means claiming originality here.

So I was giving a seminar, my first serious talk since earning my PhD the year before.  Consequently,  I was a bit nervous.  But the subject matter was so wonderful!  As part of my talk, I prepared a large Fernbach flask with marine nutrient broth, inoculated it in the early morning with a brightly luminous microbe, and let it grow a bit.  By the time I began my seminar, the culture was glowing quite well.

During my talk, as an illustration of bioluminescence, I held the flask up to my face so that (in the darkened lecture hall) the audience could see something like the spooky image above.  A nice "stunt" to illustrate a point.

Except a high school student, visiting, raised his hand.  Interestingly, he didn't know that it was unusual to ask question during a seminar.  But he was clearly excited by something.  So I called on him, in the middle of my seminar.

"I can't see through the culture in that big flask," he said.

There are huge numbers of bacteria in every milliliter of that broth, I replied, and they scatter and block the light.

"Yeah," he replied, squinting.  "So how does the light the bacteria make get out?'

I stopped cold. 

I had never, ever thought about that.  It was a nearly perfect question, from someone who didn't know about mixed function oxidases, fatty acid recycling, and the physics of emitted light.  I thought it was a lovely, lovely question and I was not in the least disturbed by it.

I stood there in the lecture hall and thought for a few moments (which yes, seemed like many decades).  And then I suggested to the high school student that he might think of the cell wall of a bacterium like the diffuser on a lamp...thus the light that was produced inside the cell was similar to a light bulb in a lamp, with the shade diffusing and spreading out the light.

And I suspect I am right (though I am no physicist).  The student seemed fine with that answer, as was the audience.

So the student's question was one of the first examples I experienced of Zen Beginner's Questions.  It would not be the last.  Embrace that high school student's enthusiasm and ask questions often!  Many times, students fear to ask questions, believing that they will be thought of being "stupid" for asking a question. Not so! As an educator, I have learned that if one student has a question, there are other students who wonder the same thing, but are nervous about speaking. Science is beautiful and complex and wonderful beyond words.  Share it, and don't be afraid find the enthusiasm of that inner child. 

Readers, please keep in mind that "I don't know" is where wisdom and learning begin.  It reminds me a little of the famed Socrates quote, that he claimed to be both the wisest and stupidest of men---stupidest for there was so much he did not know, and wisest because he was aware of the fact.  Taking a clear look with "new" eyes always helps.  The late science fiction author, Isaac Asimov, famously pointed out that:

"The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka” but 'That’s funny...'”

So embrace the beginnings of learning with enthusiasm.  Put aside ego (which, though it costs nothing, is among the most expensive of bad habits).  Become excited about how science uncovers the universe around us.

Saadat A. Khan noted the following about this ideal of the Beginner's Mind:

"Beginner's mind embodies the highest emotional qualities such as enthusiasm, creativity, zeal, and optimism. If the reader reflects briefly on the opposites of these qualities, it is clear to see that quality of life requires living with beginner's mind. With beginner's mind, there is boundlessness, limitlessness, an infinite wealth"

And embrace Shoshin with your classroom, your professors, and your family and friends.  You will be the wiser for it.  Students, ask away...with enthusiasm and joy!

A Hiatus...and Rules in Academia...

So, yes, it has been a while since I posted on my blog. Apologies all around, and I will try to post much more frequently.  

Soon after the end of my Microbiology class last semester, my father became quite ill.  I have been quite worried about him since the death of my mother in October; his hospitalization and long convalescence made me fear the worst.  My father is strong and wise, but is not young.  After quite a scare, my father is better now---which is very good news.   

As the new semester dawned, I had a large freshman course with which to deal.   My large course, with 48 students (which is not large by RO1 standards, I realize) is a bit of an adjustment; I had not handled the logistics (grading, primarily) of that number of students in some time at Puget Sound.  But I am starting to catch up! 

To that end, a quick post, about life in academia, and some “rules” for research with students.

Over the years, I have made so many mistakes as I progressed through academia that I cringe a little, remembering.  I don't have a time machine to go fix anything, but I have learned a few lessons.  Thus, I have some "rules for research" and I also have some information from a former colleague of my wife's at UW-Tacoma to share.

The rules are not necessarily complete, nor do they necessarily apply to everyone reading this.  Still, I think it is important for any academic to think about these rules, and maybe to pass them along to other academics or folks considering a career in academia.  So I thought I would share them.

First, something from my wife's colleague at UW-Tacoma (Beth Rushing, Former Vice Chancellor for Academic Affairs).

"Five Things I Wished I Had Known When I Was Beginning as a Faculty Member"

1.  There is a hierarchy among faculty members.  Respect it.

2.  You can be friendly with students, but they are not your friends.

3.  Sometimes you have to say "no," close the office door, and/or work at home.

4.  Everyone's job is important. Be nice to the staff in your program.

5.  Your job is not your life.

These rules are perceptive and true.  #2 always cuts me to the quick.  It is true that some students can become friends, but not initially. If I were to add anything to this list it would be simple:  stand by your ideals in a calm fashion.  We all have trouble with disagreements; learning how to be civil about dissent is important.  Avoiding disagreements does not help (as I have learned to my sorrow repeatedly).  Also, there is a difference between honesty and tactlessness; many people confuse the two. 

I like Dr. Rushing's rules.

Even though I am not working at a PhD (or MS) granting institution, and only do research with undergraduate students, I have worked with a few.  I have sent about 14 of my serious undergraduate research students off to PhD programs, so I have some experience with the joys and sorrows of research at primarily undergraduate institutions.  So here are my “rules.”

"Martin's Rules of Research"

Rule #1:  There is one ego per lab (and it isn't yours).

Rule #2:  Research projects sometimes appear to actively resist investigation (I take it a little personally).

Rule #3:  Never forget that there is a "re" in the word "research."  If you cannot repeat the experiment, it isn't science.

I teach all of my students these rules, and I have plaques with #2 and #3 up in lab. 

Rule #1 is amusing to me.  Few undergraduates laugh when they hear it, but everyone with a PhD does!  I know I have seen people get into real trouble forgetting #1, and I have struggled myself with it.  It’s not a “the PI is God” kind of concept.  It is a reminder that none of us “own” our research projects! 
  

Rule #2 has certainly seemed true to me, over and over again as I work with "undomesticated" microbes.  It's like the microbes are snickering at me on plates and in 2059 tubes, when I turn my back.  Fair enough:  it just makes me more determined!  And Rule #3 is a great, great thing for students to remember.  I well remember a former student getting a tricky enzyme assay to work.  "Did it!," she exclaimed.  "Great," I replied.  "Now do it three more times."  The student was confused at first!  But the ability to repeat an experiment successfully (with different hands) is at the core of good science, in my opinion.

My rules are all based on painful yet instructive lessons from my own life in academia.  Everyone is different, of course.  You know the saying:  YMMV (your mileage may vary)!

Thoughts from My Class on Small Things Considered!

Here is a quick post, while I am trying to learn some bioinformatics at Argonne National Lab.  

My thoughts about teaching microbiology at a small liberal arts institution, and what some of my students thought about microbiology, appeared today in the ASM sponsored microbiology blog, "Small Things Considered."  I hope that the post gives a flavor of the kind of classroom I try to create, and the experiences my students hopefully gain.

You can read the essay here.

An Inspirational Note Worth Reading: Grace in Teaching!

Teaching has its ups and downs, like any other profession.  It's a great feeling when a struggling student does well in class, and shows the excitement we try to teach regarding a theme or concept.  It can be sad when course evaluations suggest that the class isn't "getting" what you had intended and we need to retool our approaches (leaving aside the less-mature commentary that happens from time to time).  And, recent magazine articles to the contrary, most educators work quite hard to do the best job we can for our students (there was quite a bit of bemusement and a bit of sarcasm regarding the silly article in Forbes, such as here and here).  Doing a good job for our students remains a moving target, even for the best of educators.  We tell ourselves that that it matters, that it is worth it.  And many of us---yours truly, for example---find it to be very much worth the time-equity investment.

But it is always good to read something inspirational about teaching, that presents new approaches, and perhaps more importantly, a new outlook.  

A colleague of my wife's, Dr. Francis Su of Harvey Mudd College, was just presented the Haimo Teaching Award at the Joint Math Meetings of the Mathematics Association of America last week.  It is a great honor to receive a Haimo Award (full disclosure:  my wife won this award several years ago...and yes, I married up).  Dr. Su's acceptance speech was remarkable.  It deeply moved my wife, and she sent me a link to the speech.  I could see what she meant!  

Dr. Su posted the acceptance speech on Facebook, and I share it with you here:

Click here to read Dr. Su's wonderful acceptance speech.

Note:  Apparently, Facebook took down Dr. Su's post as spam(!).  No matter; Dr. Su kindly created a website with his talk for us all to appreciate.  I changed the link above so that it will take you to his new website.  Apologies for Facebook's, um, attention to spam.

If you are an educator, or a student, or interested in teaching or learning, please read this speech.  It is on the subject of "grace" in teaching, learning, and growing.

Richly deserved applause to Dr. Su...and not simply for the prestigious Haimo Award.  But for being willing to share his outlook and positivity with all of us.  

His students must be very, very lucky!

Educators and students:  consider the grace in your life.  And increase it with others.

More about Microbial Literacy!

Just a quick post.  I have long believed that microbiology needs to be presented in the Biology curriculum, earlier and in more detail.  It's fundamental. And I find that the typical media (as opposed to science journalists and bloggers) in particular can really confuse things revolving around microbiology, and that isn't good for education or the public at large. 

A student from last semester's microbiology course sent me a link to this video, a promotional spot about Boise State University, shown during a football game.  

I was delighted to hear the young woman mention that Boise State, to her, could mean "quorum sensing."  Fantastic!

But then, I read the press release that mentions that spot, and its "shout out" to Microbial Goodness.  I put my head in my hands:

"Quorum sensing is a system of stimulus and response correlated to population density.  The Department of Chemistry uses it to study bacteria such as the West Nile virus in its research work on viral vaccines."

Oh, my.  West Nile virus, of course, is emphatically not a bacterium.  So I went to my good friend Google.

I believe that the promotional spot is referring to Dr. Kenneth Cornell at Boise State University.  His research covers quite a bit of ground, but he does study quorum sensing in some of his research, and also is involved in working on a West Nile vaccine.  Somehow, these two items became linked by the PR department?

It's common to read, in everyday media, the confusion between "bacteria" and "viruses."  So it is important to push for "Microbial Literacy."  This is a good example:  the well-intentioned effort to promote science was laudable, but the details were incorrect.

So I urge public relations offices producing these kind of spots to check their work carefully, so that their hard work will have the intended effect:  helping the public to see the value of science in their everyday lives.