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."

The Dynamic Duo and Their Microscopy Minion (or: Anatomy of a Harvest)

Ladies and Gentlemen, your cast, in order of importance:

The Dynamic Duo, a.k.a. the Able-Bodied Assistants, a.k.a. the best money Holly ever spent on science
The Microscopy Minion, a.k.a. Holly -- and her bloodshot eyes, too

The Backstory:
Many weeks ago, in a land far, far away, through the mysterious portal of Skype, Holly and her thesis committee members conferred.

"My, what a fine set of data we'll have," they remarked as they contemplated the upcoming harvest of more than five hundred Douglas-fir seedlings. "And we'll have a whole bank of little seedlings, all with their own tiny root system communities of ectomycorrhizal fungi. Whatever shall we do to torture them next?"

Seedlings waiting to be victimized. Note the adorable straw-
and-sticker labeling scheme, which cost S. and I an afternoon.

"Well," said Holly, feeling too ambitious for her own good, "Let's do something high-risk."

"Well," said Holly's advisor, "Let's do something involving community assembly."

"Well," said the NZ team, "Let's do something involving conifer invasion risk."

"Well," said the Stanford crew, "Let's do something cool."

"Teach me how to Dougie"

Six months ago at a beach cleanup day, I learned from a local DJ -- and about 100 dancing middle-schoolers -- about a new dance called the "Dougie."

As someone with little demonstrable sense of rhythm, I'll leave it to you to look up the YouTube videos and learn the moves.  But what I can teach you here is a different, nerdier form of Dougie-ing.

Seventeen hours, two plane flights (complete with early meal delivery thanks to my new vegetarianism!), and one skipped Wednesday (thanks International Date Line!) after leaving San Francisco, I found myself in a newly-renovated Christchurch airport. A very generous J. had come to greet me as I exited security, in spite of having just flown through himself after returning from a stint in Australia just a few hours before.

"Well, are you game to just head straight out to Landcare, then?" he asked.

And off we went!

I was excited to see the progress my little greenhouse buddies had made in my absence!

Each one of the 264 pots holds two Douglas-fir seedlings,
most of whom seem reasonably delighted by their surroundings.

The 190th Hole (Anatomy of Soil Sampling)

The past week -- and the week to come -- are all about digging.  More precisely, they're about hammering a short segment of PVC pipe into the ground, and then digging.

K. and J. extracting samples from a grassland. You can see a
pine plantation in the background, and a wilding Douglas-fir
just behind K. (in the purple shirt). The white tube in J.'s hands
is a newly-extracted soil core.

Together with the help of K. (who knows all the best ice cream spots on the South Island) and J. (who's generously loaning her strong arms and back in the name of seeing more of New Zealand), I'm collecting soil samples for a greenhouse bioassay (a glasshouse-based experiment using living organisms to test the properties of an environment).

This experiment is the natural complement to my survey of fungi infecting existing seedlings. In this case, I'm collecting soil from the same three canopy types (grassland, native beech forest, and Douglas-fir forest) at sites spread across the South Island of New Zealand (rather than the few local sites at which I collected my seedlings).  I'll plant Douglas-fir seeds in these soils, allow them to grow in the greenhouse for 6 to 9 months under the watchful eye of some helpful Landcare folks who will keep them happy and watered for me, and then harvest them to find out what fungi from the soils colonized the seedlings.

Teaching a sprinter to run marathons (Anatomy of lab work)

I've always been an endurance athlete.  Probably because I'm just plain slow, and you can hide that a lot better in a 5K than in a 100-meter dash.

This Douglas-fir seedling has lost its chance to take over the world.
Or at least, the surrounding native forests. 

For the most part, after more than a decade of semi-competitive running (though over the last few years it's been more about the pleasure of stretching my legs over a few miles than about lowering personal records), my brain has been molded into that of a distance runner.  I like to stick things out, I like a certain amount of pain (I can picture Mom and Dad making their 'self-flagellation' gestures... thanks for the emotional scarring, guys! :), and -- according to Dad, anyway -- I have a reasonable degree of mental toughness.

But in some things, I will always be a sprinter.

To some extent, I espouse Hemingway's "Live hard, play hard" dogma: I have a tendency to throw myself into science and work feverishly for a few weeks or months, then wear myself out and collapse in a fit of TV-watching, elaborate-meal-cooking relaxation.  (Err, I guess that's not really relaxation... more like throwing myself into something else, equally intensely.)

In addition to seedlings, we also collect any sporocarps (mushrooms,
the fruiting bodies -- a.k.a. the physical structures that release spores,

the reproductive part of a fungus) that we find in the field.  These are

brought back to the lab for DNA sampling, photographed, and dried.

I've never been very good at pacing myself when it comes to work.  So it's no surprise that, where we said we'd collect 15 seedlings per canopy type, we came home with closer to 30.  And now, with bags and bags of samples piled up in the freezer, I'm feeling some perturbation, which is currently manifesting itself in nightmares in which I open the door to the cold room and am instantly toppled by a tidal wave of Douglas-fir seedlings that come pouring out.  (Silver lining: This is a much better dream than last week's, which featured an unfortunate encounter with a band saw while cutting sample tubes for the second half of my field work.)

As I know from experience, there's only one cure for this dream-inducing stress: Getting to work! With one sprint into the field over, it's time for the sprint to finish up lab work before the next phase of my project.  Here's how it's done.

Orion is upside down! (Anatomy of field sampling)

On Monday night, to celebrate the completion of the field survey, I stayed up long past sunset (working on this column, actually) in order to check out the Southern Hemisphere's stars.

One of many, many Douglas-fir seedlings we've collected in the past weeks.

It was a remarkably clear night up in Hanmer (location of the Hanmer Hot Springs, which we skipped, and one of the worst wasp infestations I've seen, which we sampled in), and the tiny town offered very little light pollution.  So I got my first look at an upside-down sky.

I only recognized one constellation, Orion (my "cellestial boyfriend").  And he was upside down.

"No, he's not!" K. said.  Though born and raised in Germany, she's been in NZ for more than a decade and a half, so this disconcerting reversal is normal for her.

"But his sword is pointing up instead of hanging down..."

Feeling troubled, I went back to my room in our rented Kiwi batch.  (We stayed overnight in someone's vacation home.  One wall of the living room was literally plastered with pictures, from which K. and I decided that the family had three children, one of whom was now married with a child of his own, and the parents loved taking pictures of themselves with statues.  And bathing in the... erm... nude.  Naughty bits safely underwater, fortunately.)  It was 10:30pm, way past my bedtime (yes, I am an old lady), and I was ready for bed.