The Adventures of the Brave Little Tomato Sauce Bottle

What would life be without a bit of adventure?

Sunrise and full moon over the Southern Alps.

With some luck, and the intensive root-washing efforts of K and F, I was able to finish my experimental harvest in time to have a weekend free to explore! Together with my new favorite travel companion -- a genuine tomato-shaped NZ tomato sauce bottle, a gift from Jamie - I took off South and West to explore parts of the South Island both new and familiar.

The Rate-Limiting Step

Must. Go. Faster.
Must. Go. Faster.

That's the basic mantra I repeat to myself as I perch next to the microscope, rapidly scanning root systems, typing data into the computer, and plunging root samples into chemical buffers.

There's a basic principle in biochemistry which says, essentially, that a reaction can only go as fast as its slowest step.

It follows the same idea as the old phrase, "A chain is only as strong as its weakest link." Or, in Bay Area lingo, you'll only get to SF from the East Bay as fast as traffic on the Bay Bridge will let you, no matter how clear highways like the 580, 680, and all the other 80's are. The rate at which cars can squeeze through the narrow trans-bay span becomes the rate-limiting step to transportation.

These days, I'm the rate-limiting step.

As always here at Landcare, I've had terrific help with my harvest. The seedlings must be carted in from the glasshouse, measured, and washed clean of dirt before I can inspect their root systems under the microscope. (We're also taking soil samples in case we want to do some further genetic and biochemical analysis.) K. works as efficiently as always, preparing the seedlings two-at-a-time and stashing them in water-filled plastic cups to await my attentions.

It takes about fifteen minutes for me to process a seedling, so I'm expecting to spend about 100 hours on the microscope while here at Landcare. Together with the time required to extract DNA (and make backup copies of the samples I'll be carting back stateside in case of issues with United States border security), I'm expecting to be rather tight on time on this trip.

As of end-of-day on Saturday, I'm through 152 of ~500 seedlings, optimistically on track to make my Tuesday flight. I've tallied 55,176 root tips, and taken 1,374 DNA samples.

Still, I haven't looked in the greenhouse at those ominous rows of Douglas-fir seedlings awaiting their turn to face the wash-and-clip treatment. When I think of heading out there tomorrow to survey progress and collect more samples, I can't help but remember a recent conversation with K.:

"So does it look like we're making any progress," I ask K. as she returns from the greenhouse with the latest tray of seedlings.

She pauses for a moment. "Err.... No."

I sigh, then grab the latest batch of washed seedlings and head back to the microscope.

I'd rather be lucky than good!

When I was growing up, my parents ingrained a bunch of slogans in me. They encapsulated valuable life lessons like "Attitude is a choice," "It's the beach stupid," and "Fly, Eagles, Fly!"

But one that Mom was particularly fond of saying seems especially resonant today:

"I'd rather be lucky than good."

(Dad's counterpoint was, of course, "Serendipity favors the prepared mind.")

Today, I'm feeling very, very lucky.

Because when I unpacked the control seedlings (the ones that, as I explained here, are supposed to stay "clean" throughout the experiment) today, I found no fungal contamination on their root systems!

My how you've grown! The greenhouse seedlings are mostly
thriving more than six months after their November replanting.

Though very preliminary, this is incredibly good news because it means that we've probably managed to catch the fungal contamination before it spread throughout the experiment. We'll know more in a few days after I've made some progress on the harvest, which is now proceeding full-speed ahead!

A Case of the (Missing) Mondays

Last month, when I boarded a plane to Canada for a math conference, I thought affectionately that I was glad that the last stamp in my passport, which expires in October, would be from my beloved Northern neighbor.

I didn't expect to be headed to New Zealand for another stamp before I sent my passport off for renewal. But, as those of you who saw me in my most frantic moments at the Ecological Society of America Annual Meeting this week know, sometimes surprises happen.

 This time, the surprise came on Monday: an email from a colleague who'd been kindly keeping an eye on my seedlings in New Zealand. "There's a fungus among us," he wrote -- or something of the sort. Or, to use another trite turn of phrase, "Houston, we have a problem."

Closeout Stats

We may not be able to trust Mayan numerology again (or at least not our doomsday interpretations of it), but you can sure trust these numbers!


Number of earthquakes felt in J's presence: 1
J's guess at said quake's magnitude: 3.6
Actual measure of quake's magnitude: 3.5

Total chocolate consumption by Holly: 7.86 kilograms
Rate of chocolate consumption: 1.43 kg / week
(...and accelerating. Sometimes I impress even myself.)

Root tips counted: >200,000
Bird bone photos taken: 201
Papers in press at Ecological Applications: 2 (woo hoo!)

Number of pages filled with meaningless algebra: 8
Number of models for tree-fungal interactions attempted: 4
Record lowest biomass of tree (in a badly broken model): -1 x 10^(76)
(Happily, my trees are behaving better now!)

Months until I return to Landcare: ~11
Grant money I must spend before then: ~$9,200
Thesis chapters that must be accepted before then: 2
Thesis chapters presently written up: 0.71394



Whether it's been driven by chocolate, good company, or successful science, this trip to New Zealand has been a spectacular one. And while I'm looking forward to getting back home to my practically-beachfront-apartment, I'm also so excited to come back next year and let you know how the wee seedlings fared!

Thanks for coming along on the ride!

"Well before I'm northward bound..."*

As I begin to pack up my five-and-a-half week stay in New Zealand, I thought it might be nice to document some of the fun the last week has brought my way. I was drawn to science because of its variability: It's rare that I spend more than a few days -- much less a few weeks -- doing the same thing. Which means that I'm never stuck on a dull task for very long, and that I occasionally get weeks like this one, which remind me how lucky I am that I get to play for a living and how much joy I get from my job!

Having finished up his seedling harvest, I spent Monday with J. at the Canterbury Museum, where I got to dust off my dSLR (which got hauled down here, telephoto lens and all, only to sit on the shelf while my point-and-shoot saw most of the action) to photograph some of the bones that he was measuring. Many of the photos will hopefully see some use as reference photos, since we posed them to highlight morphological differences between species. 

Bird-brained?

I absolutely love going behind-the-scenes at museums, and it was so cool to get a glimpse of the avian collection -- especially some enormous Moa bones!

And if that weren't enough, I also got treated to a couple evening trips to the seaside, once with K. to enjoy a bottle of our favourite wine, and once for a nice long run, as the shadows slowly stretched out in the lingering summer dusk. It's going to be hard to adjust to the short days of the Northern Hemisphere winter next week.

Sumner: the perfect spot for a beach run!

Fir is Murder! (Or: The Value of Scientific Collaboration)

About year ago -- before I did any field work in New Zealand; indeed, before I was even certain I'd be working on Douglas-fir in New Zealand -- I went for a run around the Stanford campus and passed a Christmas tree lot.

A lifelong tree-hugger, I was reminded of my annual childhood distress at the start of each New Year, as my Dad and I, walking around the neighborhood, bore witness to the ignominious disposal of many a family's Christmas tree. (We'd always had a lovely little artificial tree, passed down from my Dad's relatives. I think this was mostly to avoid the myriad cleaning joys of a tree shedding needles everywhere, but I chose to interpret it as my family's deliberate efforts to save baby trees.)

I mean, we wouldn't have these beautiful Canadian running
trails if someone cut down all these trees for Christmas!
(Err... let's not discuss the logging situation in B.C.)

When I got home from my run, I told Luke about the horrors of the Christmas tree lot, and he told me that every single year, his family had a lovely real tree, and that it wasn't Christmas without its delicious conifer smell permeating their house.

"Well," I spluttered. "Well... That's twenty-five years of murdering baby trees for you!"

Several days later, I'd come up with a slogan and was feeling very clever about it. "FIR IS MURDER!" I'd bellow at Luke every time one of us entered or left our apartment. (Fortunately for him, I have the memory of a tunicate, so I didn't keep this up for long.)