Damned Peas (statistics later)

Back in the day, when I was a full time research nerd, I would sometimes dream of doing experiments in my garage.  Ok, at the time we didn’t have a garage, but my desire was to do science on the cheap.  No more grant deadlines and all that.  No more feeling guilty if you left lab before 9pm or “only” came in for an hour or two on the weekend (research is really best suited for single folks sans kids IMHO).  I loved being in the lab and actually doing science, but there was a definite conflict between that and being a normal husband and dad.

In my fantasy, I would have some sort high/low tech setup (centrifuges powered by exercise bikes… someday graduating to steam driven-Rube Goldberg-automation).  I dreamed of asking questions that were both important enough to be publishable but obscure enough that no one else cared  (allowing me to ignore the pedal powered centrifuge for weeks without fear of the competitors, who never seemed to get off their own exercise bikes).

There are a few standards this research must fulfill:

  1. Must fit into the learning objectives of my classes in a direct & obvious way.
  2. Must be so simple and robust that even that rare student who doesn’t listen to directions has a high likelyhood of getting meaningful data.
  3. Must fit into what I am doing right now.  My colleagues and I are extremely busy, teaching is our first priority and things that do not directly involve teaching tend to get put off.
  4. Must not take more than the ~15 minutes of extra time I have each day.
  5. Must have the potential for students to think of their own questions and test their own hypotheses (because having students repeating “experiments” for which we know the outcomes makes me want to shove pencils through my eyes).
I think I have found it

The very last thing I did in my professional research career (while working for the most brilliant (and nicest) boss ever) was to mess around with different chemicals trying to screw up the infectious cycle of retroviruses (HIV among them).  One of the chemicals  we used was juglone:

Its effect on retroviruses is a separate (yet incredibly important) story.  The most important thing for me now is that my boss impressed me with the knowledge that juglone is made by walnut trees (thus the family “Juglandacea“, which includes hickories, pecans and walnuts).

That’s where this stayed for a couple of years.  I got this full time teaching job, we moved out here, I taught, I graded papers, I worked on committees, I slept,  I worked on committees.  Every semester though, I managed to sneak out into the forest.  With my classes, with my co-worker Todd (from whom I am obtaining an informal education in what can only be called natural history), by myself.  When you’re out there with your eyes open you notice things.  In the picture below (from our forest), compare the Black Walnut (green arrow) with the pine tree in the background (red arrow):

Who needs more personal space?  Your damned straight man, that black walnut is all “honey badger secretes a toxic chemical and KILLS its neighbor’s plant babies”.  That pine has all kinds of plants growing right up under it.  The forest has an amazing ability to invade and push into new areas… I try to impress this on my students as we cross from the manicured lawn through the *wall* of greenery that is the edge of the forest with the question: “What do you think would happen if they stopped mowing this lawn?”.  Black walnuts resort to chemical warfare to keep their neighbors away and juglone is a big nasty in their arsenal.  Honey badger wouldn’t stand a chance against a black walnut.

There is quite a literature on this, its called allelopathy (which roughly translates to  “kill anything that isn’t me”).  There are lots of people having their students doing similar experiments with different plants.  There are so many places to go with this.  To start, this semester I blended up different parts of a walnut (not the one pictured) and had students test its effect on the germination of tomato and corn seeds (repeating published data from the 40s).  To butcher some metahpors, tomato seeds are quite the hot-house flower:

Infectious disease is my background, so whenever I want to know how much of something is present, I dilute it several times and see which dilution gives me 50% of whatever it is I am looking for.  If you are working with a virus or a bacteria in petri dishes, this is called a “TCID50” (tissue culture infectious dose 50%).  If you are infecting mice or other living organism, this is called an “LD50” (lethal dose 50%).  So naturally I dilute out my extracts and look for a GID50 (germination inhibition dose 50%).  It sort of works:

It dilutes out!

Things were going great.  Students were doing real experiments, counting, graphing, not falling asleep. The chemistry professors seem game to having their students do some chemistry on this. Then I try to move to a cheaper seed after Jim (professor and colleague who has the best ideas and the calmest night-DJ voice I have ever heard) points out that tomato seeds are actually pretty spendy.  So I try some peas after he buys me a bunch from the farmers market.  A negative control, something besides water that doesn’t affect seed germination, would also be nice, so I blend up some sweetgum leaves (what could be more harmless and friendly than a tree named sweetgum??) and try that.  (spoiler alert, I am aware that even had sweetgum extract not affected germination this would not have been a good negative control, but its going to be hard to find a genetic knockout black walnut lacking the ability to make juglone, so humor me).  I will leave you with a picture of the results (last pictures taken in our living room yesterday).  Obviously, the peas are throwing me a curve ball and sweetgum trees are honey badgers too, but hell, this is fun.

What I do with my spare time.


About SubOptimist

I am an Associate Professor in the Science Department at Georgia Perimeter College, Clarkston. I teach introductory biology courses at both the majors and non-majors level in addition to microbiology. Previous to that I spent 7 years as a postdoctoral researcher on different viruses. While I don't miss being on the "grant treadmill", I think better when I write and miss writing up data for papers and grants; this blog helps me with that a little. And sometimes my kids' insanely funny and cute antics need to be shared with the world. Any view expressed in this blog is that of me personally and not Georgia Perimeter College or the GPC Clarkston Science Department.
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