A Trip to Jasper Ridge with Biologist [B.CI.1] who works with Yellow Starthistle (Centaurea solstitialis)

1-5pm, October 29, 2004


On Friday, 29 October 2004, I took a trip out to Jasper Ridge Biological Preserve with a biologist who was referred to me by B.CI.0.  I suppose for anonymity’s sake we’ll call her B.CI.1 (my naming scheme reminds me of an Ayn Rand book I read once, but that’s for another time). 


She is currently working on a project to determine what factors affect the invasiveness of Centaurea solstitialis, the Yellow Starthistle.  One factor she is looking into is the effect of slugs that prey on starthistle seedlings.  She hypothesizes that in areas where slugs are plentiful, starthistle are not.


She has set up 8 sites with varying parameters to test her hypothesis.  In each of the eight sites, there are 2 x 2 plots where starthistle seeds were left to germinate.  Plots can be invaded/non-invaded, and exclosed/non-exclosed.  Each site has all four possible plots.  An invaded plot is placed in an area where starthistle is plentiful.  A noninvaded plot is placed in an area where starthistle is rare (or pretty much nonexistent).  A plot that is exclosed has a ~5 cm diameter plastic tubing shoved into the ground (couple centimeters deep).  This exclosure prevents slugs from getting to the seedlings.  A plot that is non-exclosed has the same setup; except the exclosure is one centimeter or so above the ground.  This does not prevent slugs from getting to the seedlings.


She planted the seedlings one week before, and has come to see how many of the 10 (in each plot) have germinated (sprouted leaves).


Side note:  There are also 6 plots (at 3 serpentine sites).  Serpentine sites are land that is on serpentinite bedrock, which affects the nutrient mix in the soil.  Serpentine areas are rarely invaded by starthistle.


I’ll probably botch some scientific terminology in my summary, but hopefully she can correct me if I am wrong.  Also, it’s useful for us computer scientists (aka “non-scientists”) to review the scientific method here: http://helios.bto.ed.ac.uk/bto/statistics/tress2.html


Summary:  We went out into the field to count the number of germinated starthistle seedlings that she had planted a week before.  There were 38 total treatments—8 replicates (sites) of combinations of 2 binary variables (invaded/noninvaded, exclosed/nonexclosed), plus 3 sites on serpentine areas (exclosed/nonexclosed).



Structured Interview Questions

From the structured interview session (conducted briefly while in the car, and at the Jasper Ridge site), I discovered the following:


B.CI.1 is a PhD student in Biological Sciences, studying Plant Ecophysiology.  She is interested in how nutrient levels in the ecosystem affect plant nutrient levels (and vice versa).  She is also working with the Global Change experiment.  There is an experiment there where the CO2, N2, etc levels are manipulated to see how they affect the plant growth rates.  There are clear plastic tubes jammed into the ground for the purposes of root imaging (the tubes are called minirhizotrons).


               As she is in her second year of the program, she must find and defend a thesis proposal by the end of this academic year.  The average length of a stay in the PhD program is 4-6 years, although few finish in 4, from what she has heard.

               She has not published any first-author papers in her graduate work thus far, although she has participated in projects that have led to publications where she is a coauthor.  That project was on climate change in California; how precipitation changes cause snowpack declines, and affect water shortages.

               The time frame for her current project with Starthistle is about one season (from this summer until next April or May).  She planted some seeds last week, and she should have germinated by this week.  Some projects are longer term, and it really depends on the season.  The inter-annual variability of weather can change the ability to go out into the field and do some types of projects.

She goes out into the field about once a week (for the Global Change Experiment).  In the field, she carries a backpack with map, water, and a pencil and paper notebook.  When asked about tools like GPS, she says many biologists use it, but she does not for this project, because the number of sites is small enough for her to remember.  At Jasper, Trevor Hebert is the GIS/GPS expert.

On her project, she is working with one collaborator, who is a Stanford alum.  This person now works on the East Coast as an assistant professor, but visits to coordinate the project with her.

On her project, and fieldwork in general, the parts she dislikes most is the tedium of actually collecting the data.  Clearly, if the work were magically automated for her, she’d be grateful.  However, she does love to work out in the field.  She says that not much can replace being in the field, because one gets so much nuanced information about the season’s growth, which plants are failing, etc, just by being there.  She likes to ask interesting questions about nutrient-plant interaction, and then finding those answers.  She likes being able to take a hike in the afternoon, instead of working in a lab (I agree).  For example, just coming out to take samples of leaf-level gas exchange is a fun task for her.  This task involves clamping an instrument to leaf samples taken in the field.

So what makes a PhD better than a grad student, and a grad student better than an undergrad, I inquired?  Experience.  Experience with the equipment was the first thing that she cited.  Many times she will have to work with some procedures and equipment, and something will go wrong.  With her experience, she will be able to recover from those errors (whether human or machine errors) more quickly and with less frustration than a less experienced researcher.

The second thing that differentiates a skilled researcher from a novice (or in my case, lay person) would be the ability to ask good questions, and design experiments that would show definitively the answers to those questions.  This is a skill that comes with experience (and education of course).


Summary:  The biologist is representative of an early-mid career graduate student, working on more than one project.  She collaborates with other researchers on the larger project, but for this project, she works only with one other (based on the East coast).  She would love automation, but will not give up being in the field.




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