Category Archives: Meta

Remembering our forebears

I like to tell a story to the BIO230 students at the start of the semester, describing why I find the science of Microbiology so endlessly fascinating. Many years ago, my father’s first teaching gig was teaching Microbiology to allied health students at the University of Delaware. He and the other Micro faculty would periodically rotate through the responsibility of a class at one of UD’s satellite campuses in southern Delaware, meaning that the family station wagon would be filled up with compound microscopes once a week. Before he’d take the scopes back to campus after the class was done, one or two of them would make it to the kitchen table, so that the family could take turns looking at what ever the class had been studying the day before, from bacteria to pond scum. I’ve wondered whether my siblings or our mother found this as exciting as the 12-year old me did, however I’ve never gotten tired of being able to see something with the microscope that was invisible without it. I point to this type of childhood experience as the start of my life with science.

Later, as I began to think more carefully about how scientists accomplish their tasks–in high school science classes for instance, and then all through college classes–Dad was an integral part of the learning process. For questions I had in high school biology, I would come to him with questions about biochemical pathways, about proteins and enzymes, about evolution. I recall learning about chlorophyll in class, and asking him later about how it worked. His explanation at the time was beyond what I was able to understand, but his gift was that he helped me to see the gaps in what I knew, showing me where I could proceed–this for me was the essence of learning.

In college and in graduate school I would send him drafts of papers that I was working on for his comments. As all former students of his could attest, Dad was very liberal, almost humorously so, with the red pen, and I suspect that some of them would be hugely frustrated with that level of marginal commentary. His written commentary was not restricted to student papers; he would sometimes buy two copies of books, and use one of them for extensive marking up inside. My papers would be essentially unrecognizable when they come back to me, however they were always better for the experience.

Recently, I’ve had the pleasure of being sent his papers for my commentary. He’d been working recently on a paper celebrating the life of Albert Jan Kluyver1, who was a professor at Delft Technical University in the Netherlands in the first half of the 20th century. Kluyver’s contribution to Biology was to put forward the notion that there exists a “unity of life”, and we can see that unity in cellular biochemistry. Kluyver put forward the aphorism “from the butyric acid bacterium to the elephant; it is all the same” which to my mind, states this idea of “unity” in an elegant and poetic manner. Dad’s thesis with this paper was that modern Biology frequently misses some of these historical antecedents, and furthermore the focus purely on genetic unity that is currently in vogue does a serious disservice and sometimes distorts that earlier work. I think one of Dad’s intentions on bringing these scientists into today’s light is to remind us that many ideas in and out of science have been considered by others before, perhaps not with the same rigor or from the same direction that we might examine them today, but those earlier viewpoints have much that they can tell us.

It is a responsibility of the scientist then to carefully identify these antecedents and to celebrate them. My father, Rivers Singleton, Jr. died this past week, and we miss him. His legacy to us is to remind us that there are always questions that lead to good ideas which provoke further questions, but by carefully and thoughtfully examining those questions in the context of what has already been studied, they can become great ideas.


1. [The title of this post is from Dad’s paper on Kluyver; I am appropriating it here, in his memory]

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Happy Birthday to BIO230

Happy Birthday BIO230

At the conclusion of testing, there will be cake

Another year, another 150 or so posts up there on the Internet. I started this project 4 years ago today, with the cryptic posting “Added something to Blackboard,” and found that I liked writing on a regular basis. As the Word Cloud over there on the right might indicate, I am fascinated by the incredible variety of microbial life, and the role that microbes play in health, in disease, and in society at large.  By and large, the vast majority of people who read this are the BIO230 students I see every day, however there is a small but dependable number who visit via links on Twitter and Facebook who have no ties to York College. There are some occasional visitors from various Internet search engines hoping to find help with an assignment no doubt, but this primarily always has been an opportunity for me to help the class extend beyond the classroom.

As all students can likely tell, I can get very excited about Microbiology, and once in a while I go a bit off topic. Things here on the BIO230 blog are a bit more methodical, however I do occasionally enjoy going off on a rant here too. So in that spirit, I hereby declare a “Lightning Bonus” which will be good through 5 PM Friday October 24th. What do you have to do? Go visit these gems from the past, and comment below on this posting about any that might speak to you too. Here are your choices:

An episode of House that pissed me off

An indirect argument I had with a colleague

My attempt to influence the 2011 elections

Evil science, carried out by American scientists

Some just plain bogus science (the recursive offer of 100 bonus points has not been claimed yet)

The state of science funding at present

This one doesn’t count for bonus, but students from last spring didn’t follow directions in this week’s lab

 

Three years of BIO230 blogging: how long can it go?

The cake is the truth!

Not enough candles on that cake anymore

This is an update of what is now an annual posting: October 24th is my anniversary for maintaining this forum as a supplement for the course/personal exercise in writing for myself. During this time, I along with three dozen students have generated almost 160 290 404 posts on pretty much any topic that happened to be of interest me at the time. It was important to me when I started this project that it would be a two-way mechanism of interaction, and the student comments and participation were of paramount importance.

I’ve had a number of postings that I’ve been particularly fond of over the past year. My new recurring feature follows the Centers for Disease Control’s “Notes from the Field” column, and there have been some excellent outbreaks over the past year.  I had an opportunity for a rant this past summer, which for long time readers was a followup to this time when I dropped the “F”-bomb in class, for excellent comedic effect. Student postings have also been very enlightening and fun, for instance this submission from Katrina this semester. And I am particularly proud of my mad ego-surfing skilz, as evidenced by this ode from an admiring student from last year. Note to all; feel free to continue to use Twitter tags #shitsingletonsays and #YCPMicro for new material in future semesters.

I’m looking forward to the next year and the coming discussions. Keep the comments coming, and if you find something neat about Microbiology in the news you’d like to let everyone know about, write it up and we can talk about it together!

Cell Biologists win the 2013 Nobel Prize!

I just saw the CNN story this morning about the announcement for the Nobel Prize in Physiology or Medicine. This year’s laureates are James Rothman of Yale University, Randy Schekman of the University of California, Berkeley, and Thomas Südhof of Stanford University. All three scientists have been classically trained cell biologists who have contributed tremendously to our understanding of the movement of material inside of living cells, which is a field I have been following for most of my scientific career (all 3 of these scientists appear in the bibliography of that paper from 1997).

I have been interested in Randy Schekman’s work for the longest, dating back to when I first started in graduate school at Case Western Reserve University in the late 1980’s. His lab was interested in dissecting the eukaryotic secretory pathway in the 1970’s, and used the model yeast Saccharomyces cerevisiae to help understand it. To accomplish this, he studied a panel of temperature sensitive mutants of yeast that had a very specific part of the secretory pathway blocked when you threw the on-off switch by raising the temperature. Because the mutants were at sequential spots along the pathway, if you made a double mutant (i.e. a mutant that had two mutations in the pathway), the resulting mutant demonstrated the phenotype of the earlier mutation in the pathway. By doing this, you could tease out the individual events in the secretory pathway using genetic tools.

I heard James Rothman give a seminar also when I was in graduate school, where he summarized the current understanding of the secretory pathway from a different perspective. Rothman’s lab was interested in the same thing but used a biochemical approach in mammalian cells. By growing large amounts of mammalian tissue culture cells and purifying individual protein components, these components could be added back together in a test tube to determine the way that they interacted with one another. I recall distinctly during Rothman’s talk when he described a tremendous moment of insight when it was realized that the genetic elements studied by the yeast cell biologists were essentially the same thing as the protein elements studied by the mammalian cell biologists.

I became familiar with Thomas Südhof’s work as a postdoctoral researcher at the University of Virginia in the mid-1990’s. His lab was interested in a phenomenon that we were also interested in: how does the process of exocytosis enable materials to be released from vesicles, specifically at the synapse of a neuron? He also used a biochemical and cell biological approach to purify components of synapses and reconstituted them in vitro to dissect the parts of the pathway. He was particularly interested in a difficult problem in cell biology, which was to understand how two distinct membranes could be fused together. This problem is not trivial. Although one would think that two hydrophobic membranes might readily associate easily with one another, it is hard to rearrange the separate lipid bilayers in two membranes to bridge each other and fuse.

All three researchers have been recognized today “for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells” using parallel approaches in genetics, biochemistry, and cell biology. Science of course builds on the work of others, and this recognition today echoes the 1999 Nobel Prize awarded to Günter Blobel, and the 1974 Nobel Prize to Albert Claude, Christian de Duve, and George Palade. Today’s recognition highlights our ever deeper understanding of the fundamental relatedness of all living things.

Welcome to Microbiology!

Portrait of Antoni van Leeuwenhoek (1632—1723).

Portrait of Antoni van Leeuwenhoek (1632—1723). (Photo credit: Wikipedia)

This is the class blog for BIO230, Microbiology. I will typically update this site several times a week, with articles and news alerts that I find from a variety of sources. Sometimes postings will be very topical to health-related issues here at home, while sometimes they may only appeal to those of us below the age of 5. Sometimes I get so angry that I use inappropriate language, other times I may just update with a cat. If you don’t want to miss a posting, make sure that you subscribe by clicking the “Subscribe me!” link over there on the right. You won’t regret it, and you may even be the first to know about sooper sekrit bonus opportunities.

Here’s the first: to add a bonus point into the new Blackboard column labeled “Bonus points,” comment in this thread with 1) the topic in BIO230 you are most looking forward to, and 2) the topic in BIO230 you are most apprehensive about. Note that it would be useful to actually look at the syllabus to do this, and to perhaps thumb through the table of contents in Bauman 3rd edition. I will not count any answer that says “all of them.” You’ve got to make this worth my time, folks.

Star Trek Into Darkness: the BIO230 review

If you are like me, you were up at the crack of dawn today to watch the “Announcement” trailer for Star Trek-Into Darkness, the new offering in the series from director JJ Abrams. This preview video is in advance of the actual “Teaser” trailer which will be out on December 17, Final Exam Day for BIO230 (sorry gang, I think I will have to cancel the Final. Just kidding). The film itself will be out on May 17, 2013, and you’d better believe that I would have advance first day tickets to see it, that is if I didn’t already have plans to drive to Ohio and back.

Anyway, the teaser trailer delivers everything that it promised; a quick series of cuts that indicate frantic action and a dire situation for the Federation. The villain of the film is portrayed by British actor Benedict Cumberbatch, who I cannot imagine has a cooler name in the movie than his name already is. The vague film synopsis that has been made available indicates that he is “an unstoppable force of terror from within the Federation.” Oh, and it looks like Spock has to go spelunking in a volcano. The only thing missing from the montage is the patented JJ Abrams “lens flare” cinematography technique. Fans of lens flare will be satisfied, as there is some in the title shot at the end. The BIO230 verdict? Five bacteriophages out of five!

Chinatown, London. Benedict Cumberbatch during...

Chinatown, London. Benedict Cumberbatch during filming of Sherlock. (Photo credit: Wikipedia)

Oh, and a personal plea from Mrs. BIO230 to Benedict Cumberbatch: Please let our teenage daughters go. We miss them, and want them to start speaking to us again!

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