Perks

Celebrating the Queen’s Birthday

In New Zealand there is a national holiday in observance of the queen’s birthday. This may seem a bit funny to those Americans out there—at least it did to me—but when you think about it, it’s kind of like president’s day. The day affords Kiwis a long weekend to go on holiday somewhere or just relax at home.

I took the opportunity to travel down to the northern bit of the South Island. We visited “the sounds” region and it was a fantastic trip.

On top of the fun and games, I was able to drive on the left side of the road for about an hour without any major disasters!

There were gorgeous vistas:

Exciting roads:

And of course, lovely sunsets:

I also found a stuffed Cincinnati Red's baseball bat in a second hand store!!

The Fabulous Feijoa

If you ever get the chance to eat feijoa (Fee-Joe-Ah) fruit in your life, take it! In my book, the almighty feijoa is one of evolution’s chart-toppers. It is tart and sweet all at the same time. You cut it in half and spoon in out. Yum!

In addition to the actual fruit, one can also enjoy feijoa lollies (aka candy) that are delicious, feijoa vodka that is odd but nice, and feijoa tea that’s always satisfying after a hard day’s work. As I had not seen them before arriving in New Zealand, I assume you can’t get feijoas in the states. This fact has set me on a mission to eat as many feijoa fruits and feijoa-flavored items as humanly possibly while here.

Walks around Wellington

There are so many great things about Wellington that it’s hard to isolate just a few of the city’s attributes as “the best.” However, one of the most enjoyable aspects of the city is the green belt that basically horseshoes around the CBD providing fantastic hiking and stunning views without having to travel any distance. For example, a few of my mates and I explored the “skyline track” that runs along a ridge north of the city.

The enzymes ate my homework!

Edgar Allan Poe was pretty good at what he did but I’m fairly convinced that his stories would have been enhanced had he spent time in a molecular biology lab. No joke. It can be truly frightening because things will just go wrong. Horribly wrong. And you might not know why. In fact—in my case at least—you almost never know why. And to figure it out takes time and then by that point you’re both behind in the work you were meant to do and late to re-do whatever it was that didn’t work.

As you may have guessed, I feel a bit like I’ve been in a Poe-esque story for the last couple of weeks (granted we had a lovely Queen’s Birthday weekend holiday in the middle of it—look for an upcoming post).

Essentially I thought I was all set to send off DNA samples to be sequenced. I had done all the build-up work and I felt really good about the work I’d done. Thiw was likely my first mistake, since the Molecular Biology Gods (MBGs) can smell satisfaction and to them it smells like skunks. Just to be cautious I tested a few of my samples to make sure they were high enough concentration to sequence. They weren’t really. Well, technically they were too low. But I thought, “well, my sequences worked before and not much has changed so maybe it’s just a mistake and it will work.”

Nope. Sequencing didn’t work. The next logical step was to test all the other samples I had waiting to get sequenced. Their concentrations were also too low. At this point I was pretty upset because we’re talking about 80 samples that I thought I was basically done with.

So what happened to the DNA? My theory is that the enzymes I added to “clean” my PCR reaction—the ExoSAP that I talked about in my “scientific waste” entry—was inexplicably eating double stranded DNA in addition to the other stuff it is meant to eat. I’m currently trying to prove this but the little mini-experiments I’m setting up to test it are on the back burner as I try to redo essentially a month or more of work in a couple of weeks—using a different clean-up protocol, of course. It’s a new art called “Turbo Science!”

Hesitantly, I will report that it’s going okay but I refuse to be satisfied with my work thus far lest I upset the MBGs again.

Today, a number of samples went off to be sequenced. So, if you want to do me a favor, cross you fingers and hope that they come out okay! =)

Thanks friends,

Ellie

Real and imagined boundaries, magical people, and the science/policy interface

Small introductory note:

Let’s be honest, people: my blog is kind of pathetic. Anemic. Atrophied. Wandering hopelessly through the desert without food or water, incapable of muttering a coherent thought. Today I vow to more than double my entries by the end of June (that kind of sounds like a campaign promise, eh?). Let’s get going!

The post:

Johnny Cash was on to something: walking the line. Yes, that sounds good. But the line I want to walk is the line between science and policy. That imaginary bureaucratic, academic, and largely psychological line that we draw between the science we do and the world that can use it.

For some people, the line is more a brick wall. It is an impervious boundary that divides two disciplines. This is embraced by some academics because it makes them feel safe. On the other hand, many scientists lament the brick wall. They do this not because they want to see what’s on the other side, but, perhaps, because they sincerely long for a day when the powerful folks living on the policy side of the wall will climb over to see what’s on the science side. This may very well be a vain hope. Let’s be frank: the folks on the policy side of the wall would much prefer—for good reason—that scientists build some kind of ramp, or whatever complex machinery they need to build to feel smart, and have a go at effectively presenting their work to the “big boys.”

And yet, some scientists have turned this brick wall into more of a semi-permeable membrane. They appear to know how to package their material and present it effectively so that it floats through small, imaginary pores in the membrane, disseminating on both side. My guess is that there are people on either side of the line who would like to make these pores bigger, easier to find, and more frequently used. Or maybe we need someone to navigate the membrane for groups on both sides.

On Fridays when we’re both free, I meet with my supervisor at NIWA to discuss progress on the project, any problems I may have, and whatever tangential topics we discover in the heat of the moment.

Yesterday we chatted about this line and how I would like to be working right at the line, or even—gasp—crossing it frequently during my career. He mentioned that what is really needed is someone whose sole purpose is to patrol the line. No, patrol is the wrong word. Negotiate the line. A liaison, if you will.

This excites me. “Yes,” I said, “I want to be that person!” The problem, he says, is that no one really wants to employ that person (at least it doesn’t seem they want to in NZ) because they aren’t really “billable.” What do they produce? What to they make? I think they make all the science more meaningful by, you know, getting it to be useful to policy-makers. Therefore that person actually makes everything better and makes the research institution an asset to the country. That doesn’t seem to be something that translates into making money, however. Also, it’s not an easy job!

He launched into the job description for someone who might want to liaise between ocean scientists and policy-makers:

--Understands ocean science…broadly…. (does anyone?)

--Knows how to get scientists to explain their work

--Understands policy

--Personable

--Is perceptive and can compromise

--Good at communicating

--Knows what the policy world needs

--Knows how the science world can help

--Basically, possesses magical powers

Whoa there!! I have to be MAGICAL?!

A moment of thought followed by: “Yes…. that’s still the kind of thing I want to do.” Now I just need to work on those magical powers.

Scientific Waste

I have a friend who recently embarked on a voyage from NZ to Hawaii on board a traditional sailing Waka, or canoe (visit the voyage website, it’s really cool!). The trip is not only a way for the participants to engage with their heritage as sea-faring peoples but also a chance to raise awareness about ocean-related environmental issues like acidification, ocean trash, overfishing, etc. Part of their pre-voyage training focused on the impact that they will have on the ocean and ways they can minimize this impact while at sea.

One of the Wakas in the marina in Auckland:

Great effort went in to planning how they might go about reducing waste but in the end, the solutions are not that complicated. They bought bulk shampoo and soap for the crew that comes in biodegradable containers. They minimized the waste that will come from the kitchen by making sure that products are in metal cans or cardboard that won’t float around the ocean for thousands of years to come. This got me thinking about oceanographic research cruises because ocean trash is a real issue and humans have to stop dumping plastic into the oceans.

As a marine scientist I’ve often wondered at the many things we do in the field and in the lab that create waste and have an overall negative impact on the marine environment.

When we go to sea, it seems that no one is paying attention to the waste we create on board because everyone is too concerened about their own scientific mission. Everyone brings their own plastic bottles of shampoo, and myriad of other toiletry products. I’ve heard stories of deep-sea submersibles that have come across trash at hydrothermal vent sites that they eventually figure out was generated on the ship. I’m hoping to talk with people in charge of the WHOI fleet and other scientists that I go to sea with about ways the ship can minimize its impact on the sea. But, most importantly, I will make a commitment to doing better myself and only bringing ocean-friendly products with me to sea. Do you have stories of waste at sea or can you think of ways that we can be better?

This is WHOI's R/V Atlantis—how can we green this ship?!

After collecting animals at sea, most of my actual “sceince” happens when we get back on shore. Certain types of laboratory science create massive amounts of plastic, rubber, and chemical waste. Because I’m interested in population genetics I do most of my work in a molecular biology lab working with hundreds of tubes, pipette tips, latex and nitrile gloves, and 96 well plates, which means I go through lots of plastic and other synthetic materials that we throw away. Lab waste doesn’t get recycled beacause it’s often covered in nasty chemicals. I’ve often wondered why no one has found a way to get around this. Is there some way to wash or melt-down and purify the plastic pipette tips? Why do we have to throw away so much plastic?

Eppendorf glorifies their "consumable products" by publishing free monthly wallpaper art for your computer, like these rt PCR plates:

There are several differences between my lab here at NIWA and my home lab at WHOI, like the use different reagents, different protocols, or different brands of chemicals for certain reactions. I’m often a bit hesitant to use something new partly because when I go back to WHOI, it’s important that I be able to replicate the work I’m doing here. But in some cases, there are alternative methods to what I’m used to that could be more effective, cheaper, or even reduce waste.

For example, there are two contrasting ways to “clean up” a gene product that we get from PCR. Essentially, PCR makes a bunch of copies of one particular gene of interest. Once the reaction is run, there are some reagents—chemicals and pieces of DNA—that we want to get rid of because they might make it harder to sequence the gene that we’ve copied. To do this, I usually use a column clean-up method, produced by QIAGEN. Essentially, there is this magical tube (see below) with a membrane made out of silica that selectively binds the DNA we want and allows us to wash away everything we don’t want. In the final step, you rinse the DNA off the membrane into a new tube and you’ve got a “clean” product. Then you throw away the columns and the all old tubes.

At NIWA, someone has suggested that I use a different method called ExoSAP, which is an enzyme cocktail that digests the small bits of DNA that we don’t want. I was hesitant to accept this suggestion, but while looking at the website and reading that it advertised itseld as the “greener method” to clean up PCRs, I realized that I should really have a go because it could seriously reduce the waste that my project produces and will likely work just as well.

I’m sure that there are many ways that we can work on laboratoy trash, it’s just that someone needs to sit down and think a bit about it. I’m going to try to dedicate myself to being more aware of the ways that my science impacts the environment because there’s little sense in claiming that I’m out to conserve the oceans if I am, in fact, doing harm to the environment in the process.

Apology Haikus

Untitled #1:
Disappointing you;
Failure to communicate!
I will do better.

Untitled #2:
When lab work fails me,
motivation alludes me.
Hard to find topics.

Untitled #3:
PCR banding
that looks like lunar landing...
Contamination?

Titled #1:
I hope you get these:
Creativity attempts.
If not, more to come.