Interview with Biologist [B.CI.8] who studies plants and how they grow in response to Phosphorous and Nitrogen content in the Soil

2-3:30pm, Friday, February 4, 2004


On Friday afternoon, Thaala and Ron went to visit B.CI.8 in Herrin Labs. She is a graduate student in her 5th year, and studies plant physiological ecology. She is exploring the difference in growth patterns between plants that live in nutrient rich soils, and plants (such as cacti) that live in nutrient poor soils.


The factor that determines the nutrient mix is the presence/absence of high or low levels of P and N (phosphorous and nitrogen).


Number of Experiments

She has been working on three experiments at the same time. One experiment is run in the pygmy forest in Mendocino County four hours north of us in California


A second experiment is run in a local area where she has ~500 plants (baby pines) that she has been monitoring. These plants are in different categories of treatment, and are actually staggered in time; they are in different stages of the experiment, due to unforeseen events. Her greenhouse work lasted for one year.


A third is where she takes census of different species, with date, site, GPS location, species seen, and any notes that she takes.


Summary: A system for keeping track of experiments and experimental progress might be useful.



The Field, the Lab, and the Office

The biologist works in three different places. On her trips to gather specimens and measurements, she will drive four hours to Mendocino County. The pygmy forest is “the field.” After a day of collecting, labeling, data taking, she will drive back to her office and lab at Stanford.

               In the field, she will have a dewar filled with liquid nitrogen, her notebook, vials, labels, and a hand lens. Samples are cut from the tree, and dropped in liquid nitrogen immediately. They are not thawed, because the nucleic acids (what she analyzes) are affected when thawed. She takes six field trips in one year (four sampling trips), about 19 person days in the field.


In the lab, there are tools for measurement (masses, gel electrophoresis machines, etc). She will bring her notebook to the lab to record data.


Her office is separate from the lab where she works. Her office is where she collects research literature, plans her experiments, enter data into Excel, analyze data, and work on visualizations, results, and papers.


Summary: The field and the lab seem like temporary work spaces, where she goes to get a specific segment of work done (collection, measurement, etc). The office is where it all comes together.


Note-Taking, Entering Data, and Analyzing It

Data is frequently encoded.  For example, species names can be encoded PNEA, TORR, … Treatments are also encoded as LNHP/HNHP… (Low Nitrogen, High Phosphorous, …). This encoding of data can lend well toward handwriting recognition software. However, it currently (according to her gut feeling) lends toward higher error rates. Entering data from her notebook into her computer takes a long time, and is boring, thus lending towards human error.

               Plus, she also says that her coding scheme may have been poorly chosen. For example, LNHP and HNHP look similar, but are totally different treatments! This would also be an issue in any system we implement.


Her experiment was also blocked out in space, as the greenhouse had a specific layout. However, she did not take a map approach to data entry (as one of our other biologists did, at RMBL). Since different pieces of the map were at different stages of the experiment, she instead just used her notebook as the log-based file system. J


She uses software called Sigma Plot and JMP to analyze her data. Initial data is imported from notebook to Excel. We should visit a session of data entry and possibly video tape and analyze this process (Thaala?).


The biologist said that she wished she had a simple method to barcode all her samples (in a human readable format) so that she could maintain links between her specimens and her data rows (in notebooks) and her excel spreadsheets. She’d love a system that could beep whenever she entered data that was suspect (for some reason or other).


Her description that the notebook organizes links essentially confirms our observations that the notebook is the central organizing artifact of biology research. She said that she doesn’t share her data with anyone. Her experiment cycle is about two years, from conception of her hypothesis, to carrying out the experiment, to paper publication.


Summary: Transferring data from notebooks is tedious, and may lead to errors. Much of notebook content is encoded (e.g., LNHP) and could lend well toward automation.


Other Stuff

We asked her “what if we had some magic computer system that could do all your tedious, work for you?”  She said that she would keep up with literature more, and probably spend more time doing the asking of questions, designing experiments, and identifying problems to solve.


A quote from her: “tedium breeds inaccuracy…”  Her lab work is tedious… so she is worried that the data isn’t all correct. A system could both help with accuracy and relieve her of the tedium by making the work take less time.