Friday, August 31, 2012

Avoiding "Centrism" in Microbiology...

In class today, I introduced my students to the intellectual dangers of three flavors of "centrism."  For good or for ill, preconceived notions impact the way a scientist looks at a research question, which can in turn impede progress or even send a scientist down some incorrect paths.  

For example, in the early days of genetics, everyone just knew that DNA could not possibly be the genetic material: it only had four types of subunits (nitrogenous bases)...adenine, guanine, thymine, or cytosine.  How then to explain the complexities of living things and the genetics thereof, given only four "code letters"?  So many scientists of that time (before Hershey and Chase, anyway) felt that proteins simply had to be the genetic material, because of their diversity, complexity, and subunit composition (twenty different types of amino acids).  It never occurred to scientists, at first, that genetic information could be read off a type of tape, so that the sequence of A, T, G, and C bases could comprise a genetic code. It took some "out of the box" thinking to move in that direction, and Francis Crick had a lot to do with it.

It even got to the point, I have heard, where scientists would posit that genes were made of "protease resistant proteins," held together with short DNA molecules---to explain the effects of protease versus nuclease on "transforming material."  Sigh.  William of Ockham would shudder.

Which brings us back to "centrisms" in microbiology.

First, most students have absorbed, via academic osmosis, a eukaryocentric view of biology.  Eukaryotes of complex, and prokaryotes (or bacteria and archaea, if you prefer) are simple.  Eukaryotes have a cytoskeleton and prokaryotes do not (except they do).  Eukaryotes have organelles and compartments, and prokaryotes do not (guess what?).  This meme alters the way that students---and scientists---look at a problem involving microbes.

Next, students are taught to be oxycentric.  High energy electrons are extracted from food, and delivered via NADH or FADH2 to oxygen as the terminal electron acceptor, using an easily memorized electron transport chain.  Except that the our microbial friends---the Small Masters---are incredibly more diverse in terms of sources of high energy electrons, diversity of respiratory chains, and their own terminal electron acceptors (consider the genius level respiratory abilities of Shewanella).  

In addition, consider the amount of ATP generated from glycolysis, versus "full eukaryotic respiration":  2 net ATP versus about 34 ATP per glucose molecule.  Yet a microscopic examination of anerobic environments---rumen fluid, mud, etc---shows many types of organisms moving quite swiftly, engaged in hectic microbial business.  Anaerobic environments are not necessarily slow or static at all!  Oxycentrism gives us a false confidence that more ATP is always better?

Finally, even scientists aware of the first two traps can also think that all bacteria or archaea are organized and "act" like E. coli.  I call this academic sin colicentrism.  Operon organization, metabolic strategies, life histories---many microbiologists see the world through "E. coli colored glasses."  And it's not limited to E. coli.

Many years ago, I studied bioluminescence in bacteria.  Vibrio fischeri, a symbiont of squid and fish, organized its lux (light producing) genes in a compact manner---the regulatory gene divergently transcribed from the structural genes.  So when I began studying Vibrio harveyi, a bioluminescent bacterium that lives as a gut mutualist instead of in specialized symbiotic light organs in animals, my colleagues encouraged me to "sequence upstream" of the lux structural genes...because the regulatory gene or genes must be there.  I doubted that, wondering if the different life-histories of the two bacteria could result in different operon organization.

And I was correct.  Transposon mutagenesis showed the luxR gene in Vibrio harveyi at quite a distance from the luxCDABE structural genes.  Assumptions are dangerous; data is more fundamental.

As I told the students, it is important to always keep in mind the depth and breadth of the microbial world, the dizzying array of strategies and approaches to life histories, the readiness of change in terms of horizontal gene transfer and DNA rearrangements.  

This is the reason that I would prefer to call my course "Microbial Diversity," rather than simply "Microbiology."  I remain in awe of my chosen field.


  1. Who knew there were "ism"s to avoid in microbiology? Which do you think is the greatest sin of the three? Eukaryocentrism? Oxycentrism (now that just plain makes me laugh)? Or coilcentrism?

  2. I think that this kind of thing is pretty common in all academic areas. The old saying is that the best discoveries are made by younger scientists...perhaps this is why: too many "isms" turning our brains to rigid concrete?

    To answer your question, I think that eukaryocentrism and oxycentrism (I thought that would make you smile) are the worst...because they choke off fresh perspectives about the microbial world. Colicentrism is a smaller problem, but still an issue to folks like me, who prefer to study "undomesticated" microbes!


I am happy to hear your comments and suggestions. I hope to avoid spammage. We shall see how that works out!