Wednesday, 22 January 2014

Kia Ora!

Haere mai, or Welcome!  You've found Holly's pseudo-travelogue chronicling her adventures abroad as she conducts Ph.D. Thesis research in New Zealand.

Feel free to subscribe the the site, join the list of followers, or repost content via Facebook or other social media.  The more the merrier!

Because I'll be simultaneously filling my family in on mundane details (like my awesome orange-and-black bedroom) and explaining my research in bits and pieces, I also welcome any and all comments (you can post them at the end of any of my entries) and questions you'd like to post.  And if you're sick of hearing about trees and fungi all the time, check out my weekly columns in the Stanford Daily, yet another mass of non-work writing I love doing!

Tuesday, 27 August 2013

Until We Meet Again (Closeout Stats)

My maternal grandfather refused to say goodbye.

Instead, his words of farewell were "Until we meet again."
Sunset on the Waimakariri near Arthur's Pass National Park. The river forms
a classic winding braid over its gravel bed, an important habitat for many
native New Zealand species, including insects and some nesting birds.
Those are the words I always repeat to myself as I pack up shop at Landcare Research and leave New Zealand once again. Just as every trip introduces me to new wonders that make me love this spectacular country more, every departure makes me long for the next return more than the last.

Eyes glued to the dissecting scope in my classic work pose.
Photographed by I.A. Dickie.
Following tradition, here's a numerical summary of this trip to New Zealand:

Root tips counted: 138,755
DNA samples taken: 3,435
Chocolate consumed in this endeavor: At least 4kg
(Did you really think I was bringing some of my chocolate home to share?)

A visitor in the lab!
Kilometers driven in rental car: 1217
Wipers-instead-of-turn-signal errors: 2
American (counter-clockwise u-turns): 1
"Correct" U-turns: 3 (I'm getting better!)

Bottles of NZ white sampled: 4 (plus a Californian pinot by Cline Cellars enjoyed with J)
Servings of fish and chips: 3 (Yeah, I'm enjoying my social omnivory... :)

Time until return to NZ: hopefully a matter of months...

Monday, 26 August 2013

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.

Saturday, 17 August 2013

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.

Wednesday, 14 August 2013

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!

Saturday, 10 August 2013

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."

Sunday, 23 December 2012

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!