Leaving my L390 Children’s Literature class in Jordan Hall, I happened to mention the assignment in passing to a  classmate. She told me that Biology is the place to be. Not only is it practical, but the experiments done in the lab are fascinating, especially with genomics.

After learning a bit about genomics through the beer article, I walked to Simon Hall 409.   I was amazed at how new the building was,  and upon walking into the lab, how neat, orderly, and clean I found it,  full of machines that spin, glass-holding areas with large beakers, freezers, and water containers with what looked like it had electrodes inside.   I could not help myself but look around at everything. All the machines had little stickers faces on them, which made me laugh.

I ran into two different post-doctoral students who explained to me that the lab was not just made for one group, but that it was sectioned off. They were going to get coffee and were in a hurry, so they could not explain the difference in the lab just then.  But they told me that they were happy that I was doing an assignment like this and that exploring the lab will spark a lot of questions, and it did.

Before I knew it, I had spent an hour walking around. I was looking at data on the wall with charts that had letters and numbers on them with what seemed like an impossible code. A young woman came up to me as said she had overheard my conversation with the post-docs.  She referred me to Daniel Kearns, the overseer of the lab. He was brilliant, she said,  and helped many of the scientists with their studies, playing a very active role in everything having to do with molecular biology and genetics. I knew this was the lab I wanted to observe!

Friday November 22, 9:00-10:30am

After speaking with Daniel Kearns via email, I learned that there really were not any large scale experiments going on, but that there were  always people around working on projects. I decided to come in as early as possible, to catch people setting up and spend as much time as I could there. The first person I happened to run into while walking again through the lab was Kearns himself.  Young, with an ear-piercing, he  was nothing like what I had expected, given his prestige.  He was very friendly and open to having me meander through the lab.  

Just talking to him made me think back to my sophomore year in high school when I worked for a brief period in New Zealand. The Katipiki Ecological Restoration Project, also known as KERP, is a non-profit organization designed to help improve the balance of nature and its inhabitants, and I was able to spend a month looking at marine life and the forest areas. My comrades back then were as enthusiastic as Kearns was about his lab and what was going on there.  But somehow over the years I had fallen into a stereotypes, judging scientists as older adults I couldn’t relate to.   

He explained that the portion of the lab that I was looking at was mainly centered on genomics. He introduced me to post-doctoral students, to undergrads who were testing out the lab to see if it was a good fit for them, and to doctoral students in the process of working on their own experiments. It was within this initial tour with its  chit-chat that I found an experiment I wanted to know more about. This experiment became the center of my entire lab experience.

November 22, 10:30-11:30 pm: What I learned about the Kearns lab

Discussion between me and Daniel Kearns

What kind of lab is it?
It is a bacteriology lab and we use genetics and molecular biology to answer the questions we ask.

What is the field of science studied within the Kearns Lab?
We study bacterial motility. In particular, we study how bacteria move over the tops of surfaces.

What are the other areas studied in that lab (others have mentioned that there are other areas)?
All projects are related to motility in one way or another. The bacteria synthesize a motor to turn a corkscrew like filament that acts like a propeller to push the cells through the environment.

• We are studying how flagellar genes are regulated and how the flagellum is assembled.
• We study how cells change their physiology when moving over surfaces and the special proteins that are required to do so.
  
• We study how a protein (that we call a "clutch") stops the flagella from rotating and prevents the cells from moving.
  
• We study how cells stop moving and form a multicellular aggregate called a biofilm.

Who uses the lab? Is it all doctoral students?
I have four doctoral students, and one post-doctoral student. We also always have at least one undergraduate researcher in the lab.

I had been in the Geology Building maybe twice before, and wasn't at all prepared for the serendipitous experience that was to follow.

I spent 10 minutes cruising up and down the halls before I just picked a door to knock on and introduce myself. The professor’s name was Lisa Pratt, and she is a biogeologist. I explained my goal to spend 10 hours with a researcher and asked if she or any of her students were performing any experiments any time soon.

“You said you’re a biochemistry major?” she asked.

I replied that I was, but thought it would be good to spend time in a field where I had no previous experience or knowledge base.

“I may have something for you that would work out very well.”

She told me about her grad student Adam Johnson. Adam was a biochemistry graduate student in her geology lab who was part of a NASA project and going to collect samples Friday. Dr. Pratt was supposed to help him, but had a prior engagement and had to cancel.

She took me across the hall and introduced me to Adam. She explained my project, and he agreed to let me come help.

“Well isn’t this great!” she exclaimed. “I had felt bad for not being able to go but now I’m in the clear, Adam has a pair of competent hands to help him, and (turning to me) you can get your project done in one day. It’s just serendipity at work!”

The Meeting

Ten minutes before I’m supposed to leave with Adam, I realize I’m not sure where we agreed to meet. It’s 6:20 in the morning, and I am roaming aimlessly through the halls of the Geology Building. As I make my way up the stairs to his office, a man comes through the first floor double doors and follows me up the stairs. When we finally get to the third floor, I turn and ask “Are you Adam?”

“Yes,” he replies with a laugh.

I had met Adam once before, on Wednesday. That was when it was decided that I would go with him to Techshot, and take some samples and prepare them to be sent off to other labs. But the meeting was brief and I had not recognized him as we climbed the stairs in silence.

“Is it just us today?” I ask him once in his lab.

“Yep, just us,” he says.

His orange truck waited at the back dock ready to go.

The Ride

Adam uses a company called Techshot, an engineering company located in Greenville, Indiana, to perform his experiment. It was an hour and a half ride and I was expecting to fill the early ride with questions regarding Adam’s research. Instead, most of our conversation revolved around things completely unrelated. I found out that he is originally from Colorado, but doesn’t like snow. He has a dog named Duke and two brothers. Both of his brothers are mechanics and one recently got married. He did his undergraduate at Boulder in Colorado, and his studies have taken him places like the arctic tundra of Canada and Europe.

Whenever an awkward silence fell, I was prepared with a number of questions related to this NASA project I was about to take part in. To start with, I asked him how he fell into this particular area of chemical research. When he was younger, Adam was always interested in space. After failing the vision component of his physical to get into the Air Force Academy, he attended University of Colorado in Boulder. While in college, he found that he liked chemistry and decided on research as a means to fulfill his interest in space science. The self-proclaimed astro-biogeo-Martian chemist now plays a pivotal role in a cross team collaborative research project.

The Research

Adam is part of the NASA astrobiology team working on the Biosustaining Energy and Nutrient Cycles in the Deep Subsurface of Earth and Mars project. This is a collaborative effort between different universities across the world to determine the stability of various biological organisms in a Mars environment.

Adam’s job is to prepare several samples, including fungus, nematodes, halophiles, nathanogens, permafrost, bacteria, arctic ice, and naked DNA in a synthetic Mars soil he created in his lab. The samples are then put into a chamber which mimics a Mars environment in terms of pressure, light cycles, atmospheric composition, and temperature. The total time in the chamber is 40 days, with Adam going every 10 days to remove samples and ship them off to their respective universities for further analysis.

Depending on the organisms that survive the Mars chamber, the analysis should give NASA and other scientists an idea of how deep to dig for life on Mars’ surface. The samples are compared to a control, which Adam has under normal earth conditions. The day that I went with him, it was the second 10-day period, so the samples had been in the Mars chamber for 20 days.

It was also the second time that Adam had done this experiment. The first time he sent samples to different research centers, the microbe containing tubes weren’t labeled and were unidentifiable after shipping.

A Day in the Lab

I was a little disappointed with the Mars chamber. It really was nothing more than a room that said “Mars” on the door, with a metal box and some tubes connected to gas canisters. Had it not had that “Mars” sign, I may have confused as part of the heating system for the building. I thought it would be much bigger for one thing…and a little more complex.

Adam took me to the basement of the building housing his control samples. The room was a cluttered lab with microscopes, tubing, scales and other instruments and various pieces covering the tables. We sat down at a hood and Adam began briefing me on exactly what he wanted me to do.

There were several small tubes in front of me containing dirt, and in that dirt were the microbe samples under study. All I had to do was find the corresponding labels for each group and stick those on the tubes. I would then pass those tubes off to Adam, who would plug them with glass wool and a rubber stopper. We did this for about 25 tubes.

Next, we had to wait for the samples in the Mars chamber to be ready. As I mentioned, the Mars chamber had similar conditions as the surface of Mars – similar pressure, temperature and atmosphere. If we were to open the chamber too quickly, it could ruin the experiment. So, we had to wait for the chamber to reach conditions safe to open.

When it finally opened, Adam had to work quickly so that the samples were not exposed to earth conditions too long. This included holding his breath. He had to remove the necessary samples and place them on dry ice.

Once this was finished, it was back to the basement lab.

In order to preserve the experiment, it is necessary to maintain Mars conditions as much as possible. So, for the next part Adam had to perform his work in a giant “glove bag.” This is a giant clear bag that has inserts for his hands. The bag was drained of oxygen by a vacuum and filled up with CO₂. Here, he did the same thing we had done earlier to the controls; he labeled the samples and plugged them with glass wool and a rubber stopper.

After all the tubes were plugged (60 including the controls and samples), Adam taped all of the tubes to cardboard and placed them into mason jars. No, they were ready to be shipped off.

The project, Adam soon told me, represents hundreds of man hours once one included the preparation and data analysis.

“Science can be so tedious and boring at points,” he said.

I had to agree.

--Maegan Ionoff

I somehow ended up on the roof while looking for Caty Pilachowski’s office. Swain West, the building that houses both the physics and astronomy departments, is a bizarre labyrinth of offices and labs. Additions over the years have been strangely illogical (for example, you can only get to parts of the third floor from specific staircases), and a person can end up in some weird places if they don’t pay attention.

Our home galaxy, the Milky Way. Photo by 2MASS=Two Micron All Sky Survey.

When the universe was born, it only contained the lightest elements: hydrogen, helium, and maybe a little lithium. But as time went on, these elements smacked into each other inside stars and formed different elements. This is called fusion, since the nuclei of the elements fuse together.

But because their insides only reach a certain temperature, lower mass stars can only make new elements up to the weight of about aluminum. To make elements heavier than that, the star has to be really hot. Like supernova hot.

A supernova is when a star blows up. As you might be able to imagine, an exploding star is a pretty big reaction, and the heaviest metals can be formed. These then get flung all over the place, where they can then be incorporated into newly forming stars.

So by measuring how much and what kind of metals are in a star, Pilachowski can tell their relative age. Younger stars would have more metal atoms than older stars.

And by using a really big telescope to look at the outer layer of the star, the metals can be identified by the lines of color they absorb. This is called a line spectra, and each element has one all its own. Kind of like a chemical signature.

Hearken back to high school chemistry. You remember that all elements have a specific number of electrons, right? And that these electrons move in discrete paths called orbits. Imagine the electrons as driving around in little cars, on little tracks. The only way they can move is to jump into another car, on its own, different track. And all of these tracks are a known distance away from each other.

The Pleiades open cluster. Photo by NASA/ESA/AURA/CalTech.

From this information, Pilachowski can learn about the origins of our galaxy: which stars are young, which ones are old. Which ones have had heavy metals flung at them by exploding stars.

Okay, so there’s no denying the neato factor in this type of research. But why does she do it?

“I really like stars,” she said, a radiant smile breaking through the cool scientist demeanor. “I’ve always liked stars.”

* * * * *

After I left Caty’s office, I jumped across the hall to talk to her research group.

Crowded into a closet-sized room (well, a large closet) were three people and six computers. As I walked in, the person in the middle unfolded his long frame to greet me.

“I’m Christian,” he said, shaking my hand.

Christian Johnson is one of the three senior graduate students in Pilachowksi’s lab, and graciously allowed me to tag along with him for a bit. He is tall and blond, with the somewhat peaked look of someone who spends a lot of time in front of a computer.

The other two senior members of the lab, Tala Monroe and Heather Jacobson, said hello and smiled at me as I pulled up a chair behind Johnson’s massive black one. And then he started telling me about his research. Overall, it took about an hour, but here’s the gist:

Johnson studies the chemical evolution in the globular cluster Omega Centauri, the largest star cluster in the galaxy. Compared to the Sun (and they compare everything to the Sun), globular clusters are old folks—ten to twelve billion years old. The stars Johnson studies are also larger in size than the Sun, about 50-100 times the radius. But at the same time, they’re smaller in mass, only about 80% of the Sun.

NGC 5139: Omega Centauri, the largest globular star cluster in the Milky Way. Photo by Martin Pugh.

Within Omega Centauri, Johnson tells me, he looks at red giants. These are low mass stars, less massive than the sun, but more than two times as old. They’re called red giants because they’re both red, and well, giant. Red giants are used because they are bright and can see them from much farther away.

A reason why they like these clusters is that they know how far away they are, and they know how bright they are. That’s important for making sense out of the data they collect.

Specifically, this globular cluster is about 5 kiloparsecs away.

“I suppose you want that in light years,” he says.

I nod. Parsecs? That’s from Star Wars, right?

It’s about 20,000 light years.

I ask him if he thinks the stars he’s looking at are still there. I mean, the light left them 20,0000 years ago! Anything could have happened since then.

But he seems less than impressed.

“Oh sure,” he says.

To collect this light, created so long ago, Johnson needs a really big telescope.

Pilachowski had told me that most of their collection gets done at either the Kitt Peak National Observatory near Tuscon Arizona, or the Cerro Tololo Inter-American Observatory near Santiago, Chile. Johnson collects his data at this site, in the Andes Mountains.

The Blanco 4 meter telescope at the Cerro Tololo Inter-American Observatory. This is the telescope Johnson uses to collect his data. Photo by Tala Monroe.

They only get a couple of nights there, and they have to stay up all night to collect their data. It’s pretty remote, Johnson said. The telescope is high up on a mountain. They sleep, during the day, at the little compound about two miles away. The site provides cars for them to travel back and forth.

“And of course you can’t turn on the headlights,” Jacobson chimes in.

This confused me for a second. Then I got it.

“Oh,” I say. “Yeah, of course.”

Of course they can’t turn on the headlights. Why go all the way to a completely remote area in the middle of the Andes Mountains, where there’s no light pollution or people around at all, only to screw up your data collection by turning on your headlights?

“So how do you see?” I ask.

You kind of don’t.

“You have to drive at about two miles an hour, hoping you don’t go off the road,” Heather tells me.

“And the dirt roads are really steep and winding. And there aren’t any guardrails,” Johnson says.

“But they do give you flashlights,” Jacobson says.

Yeah, good thing.

They get about three to six nights per semester, or six to ten nights per year to collect their data. And then the rest of the year, they study what they’ve collected.

The data that Johnson collects is about the amount of metals in the red giants of Omega Centuri. He looks at the line spectra of a lot of different metals, but uses iron as an indicator of the composition of the metals in the star. Plus it has several lines, so it’s easy to pick out.

Once he locates his lines, he measures how big they are, specifically their depth and width. This tells him how many atoms of each element are in the star. He plots this information for the many thousands of lines.

This takes…a while. To get meaningful data, Johnson first has to clean up a bit, doing things like converting units and other housekeeping like that. This can take anywhere from a few days to a few weeks. Then he gets down to looking at the lines themselves. There are around 1000 stars, and about 30-50 lines per star. So there are tens of thousands of lines total. Each star takes about five to ten minutes to work on, so you can do the math there.

Johnson inside the focus of the Blanco 4 meter telescope. Photo by Tala Monroe.

Once he gets all this data worked out, he compares it to the Sun. This gives the relative chemical composition of the star, which in turn tell Johnson what’s going on, evolution wise, in that little section of the galaxy.

Johnson has been looking at line spectra of about 1000 giants in his global cluster, which is the largest detailed study for a single cluster so far. There are four or five known populations with different metal contents for him to use as a kind of staring point. But what he’s trying to figure out is how exactly chemical evolution happens—if more supernovas have gone off, and polluted stars with heavy metals, and which stars produce certain elements.

So all this he figures out while sitting in front of his computer, day after day. But the big picture?

Johnson collects the light that left 20,000 years ago from something that’s 95,870,000,000,000,000 miles away with a really big telescope in Chile. Then he brings the enormous piles of data back here, and analyzes it over the course of many months. From this, he can extract details about the origins of our galaxy.

Give or take.

Friday, November 21^st, 2008. 10:02 am. Still Earth.

It’s group meeting time.

All academic labs in the entire universe have group meeting. It can mean different things for different groups, but in general it’s a time for the whole research group to come together and talk about their work. In the Pilachowski lab, it means that everyone assembles—Johnson, Monroe, Jacobson, Pilachowski, and Maria Cordero, a first year graduate student from Chile. They all talk about what they’ve done in the time since their last group meeting (Johnson says they’re a bit on the erratic side, with people winging off to remote telescope locations now and then).

Johnson, Monroe, and I get assembled in the conference room down the hall from their office. Desks are pushed together to form a makeshift table in the center, and the walls are covered with blackboards and whiteboards and pictures of galaxies.

Pilachowski breezes in a few minutes later, looking fresh but tired already.

“I have meetings at 9, 10, 11, 12, 3, and I teach at 1:20,” she tells us.

As chair of the astronomy department, she’s got a lot of administrative duties to deal with. So she gets right down to it and starts talking to Johnson about the proposal he’s just finished working on.

“I thought the proposal surprisingly turned out well,” she said.

It’s a joint proposal, to submit to the National Science Foundation (NSF). Researchers in academic environments all have to apply for funding through either public or private sources. The NSF is one of the big ones, but also one that’s been hit by budget cuts in the last few years.

It’s a collaborative proposal with scientists at UCLA, Johns Hopkins, and Ohio State, and Pilachowski thinks they have a good chace of getting it funded.

“It’s a pretty strong scientific group,” she said.

It would be the first big comprehensive look at the bulge, the thicker part in the center of the galaxy, she tells me. Pilachowski thinks their chances of funding are about 50/50.

“You might have a post-doc,” she says to Johnson.

While Johnson is only a fourth-year grad student, he thinks he’ll finish his dissertation in about a year. That makes him a bit of an overachiever, since it normally takes astronomy students six to seven years to finish up. But that also makes him mindful of what he’s going to do next. Johnson ultimately wants to go into academia, to be a professor. But he needs to do some post-doctoral research first. And if this grant goes through, he’ll get one, because a salary for him is written into it.

From here they plunge into Johnson’s latest data. He hands her a graph, of some of his data plotted against some data from another research group on the same type of system.

Pilachowski looks over her glasses and tries to explain this project to me.

A compilation image of the Keplers supernova. Photo by the Chandra X-ray Observatory.

“We’re trying to figure out where the elements are made,” she says. “So we’re trying to find the previous generation of stars.”

Sodium and aluminum are produced mostly in explosive reactions, she says. These tend to have really high temperatures.

“Around 200 million,” she says.

I ask for the units.

“Doesn’t matter,” she quickly answers.

Ah. Good point.

Generally, temperatures are reported in Kelvin, which is degrees Celsius plus 273.15. But when something is 200 million degrees, difference like 273 means pretty much zip.

But once those heavier elements like sodium and aluminum are formed, she goes on, other elements can formed through little side reactions.

“There are lots of different things going on,” she says. “It makes it complicated to untangle."

She goes back to the graph in front of her, and notices that one set is a lot different than the others. Pilachowski thinks it maybe formed in different part of cluster, but Johnson shrugs. She says she’ll look at it in more in detail later, then asks what else he’s got.

“I’ve been comparing my data to previous studies, and working on the paper,” he says.

The goal of research groups, besides getting grants funded, is to publish their results in academic journals. Johnson’s had four published so far, three of which he’s been the first author on (which means he’s done the majority of the work).

“I should have everything but the conclusion by next week,” he continues.

“Fantastic,” Pilachowski says. Then she turns to Monroe.

Monroe talks for awhile about changing some of the parameters for working up her data, how it seems to be giving her somewhat better numbers. Then Jacobson talks about some of the work she did a couple of years ago, how she’s found some interesting stuff. Then the conversation moves around to the trip back to the telescope in Arizona that she’s getting ready to leave on, to collect more data for this project.

Time exposure of the Kitt Peak National Observatory. Photo by NOAO/AURA/NSF.

At this, Pilachowski puts her head in her hands.

Jacobson looks slightly alarmed.

“Will it be tricky to combine new data with the old data?” she asks.

“What we saw when we were there last week was scary,” Pilachowski says, her voice muffled by her hands.

She and Monroe were just down there on a collecting run just a few days before.

“The lens is in the wrong position, and it’ll have to be remachined,” she says. “It sounds like a problem we’ll have to deal with for awhile.”

The settings for the telescope have been changed since Jacobson collected her last set of data. This is bad, because if she sees some kind of difference in the new data, she won’t know if it’s a real difference, or if it’s different because her parameters were different.

“My guess is your resolution’s going to suck, which is not good news,” Pilachowski says.

Jacobson is supposed to leave in two weeks. Pilachowski suggests that Jacobson might have to reconsider what she’s going to try to observe, or have alternate plan. She’s annoyed that they made changes right before Jacobson’s last run, because it’s the last time she needed to get data at the same parameters.

“I wish that they’d waited just a few weeks,” she says. “I have a right to be totally totally pissed. I got no official word about it.”

And then Pilachowski looks at her watch, and sees it’s almost time for her next meeting. Off she goes, and the group trickles back to their office.

* * * * *

Saturday, November 21^st, 2008. 1:13 pm. Somewhere in space, looking down on earth. At least that’s where we’re supposed to be in our imaginations.

I’m late, so I try to slip discreetly into one of the teaching labs in Swain West, breathless and hot in my coat and hat. The room is pretty full. All around the perimeter are adults, looking amused/interested at the circle of about eighteen small girls, all wearing matching shirts or brown sashes.

Tala Monroe stands in the midst of the short people. She smiles down at the mass of assembled Brownies, showing deep dimples.

“So if we’re laying on our backs, looking straight upwards, and the sun is directly overhead, what time of day is it?” she asks.

The room gets quiet as the group of six and seven-year-olds stop to think.

“Nightime?” offers one little girl in a pink shirt and gold-rimmed glasses.

“No,” Monroe says. “Try again.”

“Day?” says another girl, a black newsboy cap perched jauntily on her head.

“What time of day?” Monroe asks.

“Noon!” someone shouts.

“Right!” Monroe says. “When the sun is directly over our heads, it’s noon.”

Part of being an astronomy graduate student at IU is doing outreach. Today, several troops of Brownies, about 80 girls in total, have come from all around South-Central Indiana for a science day. There are several rooms set up with activities in different disciplines. We’re, obviously, in the astronomy room. Monroe has the girls turn to their left. They all stick hands with a ‘W’ written on them into the center of the circle. The hand with ‘E’ on it points out.

“What time of day is it now?” she asks.

“Sunset!” someone shouts.

“Right!” Monroe answers.

Monroe is the outreach coordinator for this semester, so she’s the one leading the activity, The Reason for Seasons. She has the girls all pretending to be little earths, with Jacobson in the middle of the circle, holding a yellow ball on her head. (That’s the sun, if you didn’t get it.)

They go the rest of the way through their teeny rotations, and end up back at noon again.

“We’ve just completed a full day,” Monroe says. “How long did that take?”

The axial tilt of the earth in relation to rotation axis and the plane of orbit. Image copyright Dennis Nilsson.

“Twenty-four hours!” says a girl in a green striped sweatshirt.

Johnson watches from the back of the room, near the sign that says “Spring Equinox” taped up to the wall. The “Autumn Equinox” sign is on the wall behind Pilachowski’s head, on the opposite side of the room. Summer and Winter Solstice signs are to the right and left of Johnson, respectively. Another sign with the word “Polaris” and a drawing of a big yellow star, is above the winter sign, just below a big clock.

The girls pirouette like teeny planetary ballerinas, going through their 24 hour day. Then Monroe tells them about the orbit of the earth.

“How many days are in a year?” she asks.

A girl in a purple shirt puts up her hand.

“About 365 and one-third,” she says.

“Um, right!” Monroe says, slightly surprised. “So we’re going to go through our orbits, while rotating at the same time.”

They start off on their course, going slightly astray as Monroe laughs helps them in the right direction.

There is much giggling. They get to their original spots, then stop.

“It’s pretty amazing what the earth is doing when we’re not paying attention,” she says, and many Brownies nod.

But we’re missing something, she says. She reaches behind her and grabs a globe.

“It’s not straight up and down, is it?” Monroe asks.

Nope, the girls say. It’s tilted. Monroe tells them that the earth is always pointing at Polaris, the north star. She has the girls hold their hands above their heads, then lean over and point at Polaris. Now twirl, she says.

They do it, again with much smiling and giggling.

“Now we’re going to rotate, while pointing at Polaris,” Monroe says. “Think you can do it?”

“Yeah!” they yell.

What happens next looks like a traffic pile-up, but cuter. They’re all running into each other, going off course, and practically falling over. Once get back to their starting positions, they calm down again.

“The tilt is the reason for the seasons!” Monroe says.

She leans over, near the Winter Equinox sign.

“My top part gets less sunlight than my bottom part,” she says, which makes the days shorter and the air colder.

She goes to each station in turn, demonstrating the amount of sunlight that falls on the upper and lower half of her body.

The Brownies nod.

“That makes sense,” says a small blond girl.

After doing another short activity at the lab tables, the Brownies file out to go to their next room.

Johnson looks a bit overwhelmed.

“Look inside yourself, and find your inner second-grader,” says another grad student, who was working at the next table.

“I don’t know if I was a normal second-grader,” Johnson answers.

But then he doesn’t have a chance to say much more, as the next group is coming in.

Over the course of the day, they’ll do this six more times. Just part of their job, as astronomy students. That and figuring out the origins of the galaxy.

All in a day’s work.

–Lauren Younis

The study of Sindbis is important not only in terms of its ill effects on horses, though. Researchers have noticed several recent strains of the virus around the world in humans, as well. The most common symptoms of Sindbis in humans are rash, arthritis, and often fever, but the virus is, at least, not generally deadly.

The goals of Hardy’s research are many, although in a nutshell they boil down to determining the difference between the virus’s replication in arthropods (flies, mosquitoes, and other insects) and mammals. Since Sindbis hijacks its hosts’ RNA, the virus can cause havoc at the cellular level, interrupting any number of cellular processes. Just what processes are interrupted depend on the biology of the host in question, since different organisms produce and use proteins in different ways. Thus Sindbis can mean death for an equine host even after taking up residence in the mosquito that bit it.

The laboratory is replete with refrigerators for biological media, lab benches, and shelves full of various chemical primers. It’s a stark contrast to the office-like behavioral psychology labs that I’m accustomed to, where frequently a few computers or perhaps a skullcap for electroencephalography are the most technical instruments. But dress here is still just as casual. T-shirts, sweatshirts, and jeans prevail over lab coats and goggles, good evidence that this is a day job and not a promotional photo shoot for Indiana University’s admissions catalogue.

Grimard shows me a few different cell cultures that to my untrained eye look unremarkable. Among them is a culture of HeLa cells. HeLa, as I learned several years ago during some leisurely reading on Wikipedia, is a cell line derived from Henrietta Lacks. Lacks died from cervical cancer in 1951, but her cancer cells are special: They are, in biological terms, immortal, able to divide an infinite number of times so long as their basic needs are met. Countless cultures of HeLa cells are still maintained today and used worldwide for cancer research.

I ask Grimard if she finds this back-story at all unsettling.

“No, not really,” she says, shrugging.

Dr. Vasanthi Avadhanula, one of the lab’s post-docs, tells me that the cell culture room is absolutely off limits, but her smile belies her tone, and Grimard escorts me inside. A refrigerator stacked with a dozen or so Petri dishes fosters some of the cell cultures the team uses as research vectors for the virus. The room is also furnished with vacuum hoods for the researchers to work in so as to avoid unwanted contamination when implanting the virus into a new vector.

Hardy’s lab uses the Sleeping Beauty transposon, a moving segment of DNA, to mutate HeLa and hamster cells. After infecting the cells with the Sindbis virus, the scientists determine which ones survive and which ones don’t, looking at genetic differences. The shelves at Grimard’s bench house a number of Petri dishes colored violet with dye and marked by their particular mutations. A violet color indicates which cells were still alive when they were cemented in place with formaldehyde, and the clear circles, or plaques, are evidence of the virus’s handiwork. A larger plaque after a given amount of time evidences fast transmission of the virus, while occasionally no plaques show up at all. The researchers can then look closely at the genetic differences between the cell cultures in question.

One of the major difficulties is that most of the important microscopic goings-on are impossible to observe directly. Instead, the lab’s technicians carry out time-honored techniques from molecular biology in order to see events on the molecular level. Grimard uses a particular series of polymerase chain reactions (PCRs) in particular. PCRs allow researchers to look at the specific parts of a molecule. Performed with high precision machines, a PCR involves tightly controlling the temperature so that polymerase—an enzyme that reads and copies DNA in nature—can make many copies of the DNA segment researchers are interested in.

Sindbis virus disrupts a cell’s ability to make the proteins it needs to survive and communicate with other cells. When this happens, a cell dies. Other cells, however, thanks to differences in their DNA—and, therefore, how they make and use proteins—might remain alive in what is referred to as a “persistent infection”. In a persistent infection, cells continue to divide even though the virus is present, as is the case with Sindbis in mosquitoes and other insects. The goal, then, is to find the host factor—the genetic sequence in a cell—that allows them to survive.

Even after two years of rigorous research, Dr. Hardy’s team has come up empty-handed–no host factor has been identified.

“There have been many problems and setbacks,” Grimard says, “the downside of research.” What seemed initially like a straightforward problem—identifying the gene that allows some cells to divide even when the virus is present—may be more complicated. Regardless, ruling out possible factors is still good science, if only because it can lead to more questions.

When first told about this assignment, I have to admit several emotions came over me. I was excited, of course. I knew it would be interesting to observe a lab. But I was also nervous. I had never watched a “real” lab in action. The last time I was in a lab was 12^th grade biology, when I dissected a cat. Still, I figured if I could stomach that, observing a professional lab setting would be cake.

After several visits to the geology and astronomy departments (where I had zero luck), I ventured to the Psychological and Brain Sciences building. While roaming aimlessly through the hallways, I noticed displays explaining psychological terms along with pictures. After just a few of the displays, I grew interested in the science of psychology. This gave me determination to find a psychology lab for the assignment

X Marks the Spot:

After "bulldogging" several websites on my laptop at home, I came across one that jumped out at me. It was Professor Robert Goldstone’s, on precepts and concepts (http://cognitrn.psych.indiana.edu/index.html). It was the colorfulness and design of the site that drew my attention. However, the detailed links and mounds of interesting information kept me there, for what seemed like hours.

I finally found the number to the lab and called it. A friendly voice came over the phone. “Precepts and Concepts Lab, this is Drew." I explained my assignment, and Drew seemed very interested. He asked me a few questions, including when it would be convenient for me to stop by. I set up some times slots and soon I was all set to observe my very first professional lab.

Meeting the Mastermind:

My first scheduled meeting with Drew was interesting. He explained to me that he was a graduate student in psychology at Indiana University and was helping Professor Goldstone on his cognitive studies. He gave me a tour of the lab and introduced me to some key people in the laboratory. I was only able to meet Dr. Goldstone briefly. He travels often and was getting ready to leave town.

I have to admit I was surprised with how friendly Dr. Goldstone was. In my own mind, I’d pictured scientist sas stuffy and nerdy. But these are adjectives I would never associate with this man. Between his friendliness and the pictures of his daughter and family assessible on his website, it was growing clear this was no rigid, self-absorbed scientist, but rather an interesting, knowledgeable PhD, who was more “normal” than stereotypes allow.

The Lab:

I have to be honest. I thought the lab set up was going to be something extravagant. I guess Hollywood has gotten the best of me. I had assumed there would be some lavish equipment and high tech security everywhere. To my surprise, the lab I observed was somewhat simple. A dozen computers lined two walls of a room, each separated by a partition. In the rooms next to the computer lab were offices where the graduate students, post doctorates, and undergraduate research assistants sit. Here they analyze data, come up with new ideas, and observe study subjects.

Teamwork:

There are no scientists in white jackets adding mysterious liquids to test tubes in this lab. While labs like this exists (on the other side of campus), the laboratories of cognitive sciences are a bit different. In a sweater and jeans, graduate students analyze data on several large Mac computers. They sit in their offices compiling and observing graphs that, while they make ense to them, are completely mind boggling to me. Dr Goldstone’s lab has been in existence now for about 20 years. It is set up in almost a hierarchy. At the top of the totem pole is, of course, Dr. Goldstone. Below him are post-docs (people who are working with him after earning their PhDs), then graduate students in the Psychological and Brain Sciences Department. Last, but not least are the undergraduate research assistants, usually seniors in psychology, whose main role is to run the many experiments the graduate students create. Then, of course, the research subjects, who are freshmen and sophomores in psychology classes.

Grad students or post-docs create experiments which they run past Dr. Goldstone in an hour-long meeting. After some input from Dr. Goldstone, they take the constructive advice and revise the experiment. After several meetings, the experiment is set to go, run by the undergrad RA’s.

I had no idea so many people went into the making and execution of an experiment. Month’s, even years of hard work are put into these studies.

The Experiment:

The experiment I observed was created by Sam Day. Day is one of the post-docs helping Dr. Goldstone with his research. The purpose of the lab, according to the RA, Kristin, was, “ to study how people take new information and apply it to tasks that seem different."

Twenty-one freshmen walked in a single filed line and found a computer to sit at. After a few minutes of the RA preparing the computers for the experiment, she gave the subject instructions, and soon the experiment began.

It was interesting to see the “behind-the-scenes” perspective of a lab. I myself was a subject for an experiment when I was a freshman, but I had never seen all the hard work that went into its preparation.

Final Thoughts:

I’m glad I was able to experience a professional lab setting. In order to be a great journalist you have to have a first hand experience about what you are writing about. Now that I am more knowledgeable about what a lab actually entails, I am hoping it will make me a better science writer.

I liked seeing how the experiment was put together from start to finish. There is so much information that has to be compiled as well as many people who help to execute it well.

A lab is almost like a team. Each person involved in an experiment, from the P.I to the freshmen students being tested, has an important role to play.

I enjoyed this experience greatly and would observe another lab in a heartbeat. It was interesting, educational, and fun.

***

1) Organization is everything… except when it doesn’t happen. Two of the first things I wrote in my notes were Meghan’s rules of “Label everything” and “Write everything down in two places.” Because many of the solutions the group makes can look similar, and because many of them are unknown compounds, it is critical in the lab to record as much information as possible. A note taped to each refrigerator/freezer reads as follows:

All items placed in this refrigerator/freezer must be labeled with your name or initials, compound identity, and date. If this information is not on the item, the Lab Gnomes will come and steal the sample away in the middle of the night!

As far as I could tell while there, Meghan followed her two rules to the letter. She had her red sharpie out all the time to write down the mass of a beaker or the identity of a solution to put in the freezer.

But, sometimes even the best laid plans go awry. Vinnie Cavaliere, another grad student in the lab, spent his Friday clearing out the freezer and testing unmarked beakers. A lot of unmarked beakers. The lab members write on their beakers with markers, and those notes often get rubbed off accidentally. So, when they have downtime, they try to clear out the freezer and identify the now-mysterious compounds.

What does this say about a laboratory? Yes, organization is essential. But, scientists are like any other person. They try to be as organized as possible, and sometimes, it just doesn’t work like it should.

2) Safety first! When Leigh first emailed me the okay to shadow in the lab, she warned me that the materials in their lab could be toxic, explosive, etc.

Accordingly, I showed up with my lab goggles, ready to avoid any toxic, exploding compounds. Signs on nearly every fridge, cabinet, or drawer warned “Irritant,” “Flammable Liquid,” “Poison,” or “Corrosive,” with helpful images of cartoon hands being burned through by cartoon liquids. When it came down to it though, I saw no such dangerous activity.

But the lab members know the capabilities of the materials in their lab.

Around the materials that they know well and have handled often, the workers in the lab can be confident that they won’t explode something. But in other areas, they are safer. For instance, when washing her glassware in an acid/base bath combination, Meghan wears a giant green glove and a lab coat to protect her and her clothes from any splashing.

As with their organization skills, scientists are like any other person when it comes to safety. Be safe, but be realistic, too.

3) Chemistry machines are pretty cool. I got to visit several of the different machines used in the chemistry department, including the mass spectrometers (http://chemfacilities.chem.indiana.edu/facilities/masspec/default.htm) and the nuclear magnetic resonance (NMR) machines (http://nmr.chem.indiana.edu).

Mass spec analyzes the mass-to-charge ratio of charged particles to identify the material in a sample. The analysis occurs by passing the sample through magnetic and electronic fields in the mass spec machine. The machine at IU is very nice and allowed us to leave our sample in line behind several others. When the sample was analyzed, the machine emailed the results to Meghan. Although the mass spec machines are cool, I got to spend more time with the NMR machines, so I know a bit more about those.

NMRs are giant magnets which can be used in all kinds of chemistry. To help identify one of the unknown compounds, Meghan and I trekked down the hall to the NMR room. When we got there, Meghan advised me to leave my cell phone and any credit cards on a table by the entrance. NMR uses high-powered magnets that can affect the usability of some electronic devices and the magnetic strip of credit cards.

The machines are in almost constant use, but we went during a scheduled “free time.” Meghan put the sample in a slim glass tube, which she then put into a holder in the NMR machine. She climbed a ladder to reach the holder and when the tube was in, the device reacted in true sci-fi fashion, whooshing and whirring as it lowered the holder into the giant belly of the machine.

I won’t pretend to know the specific mechanics of the NMR machine, but the end result was a reading of how the substance in the tube reacted with the magnetic field around it. By reading the results, Meghan could figure out what substances were in the sample she had made. A great benefit of the NMR machine is that the scientist doesn’t need to submit a pure sample. Meghan knew that there may be some ethanol in the sample, since she had used ethanol as a solvent earlier. But, since she knows what results ethanol produces in the NMR machine, she can ignore any of those spikes on the readout.

Electronics are the kind of thing that it’s easy to take for granted. But if we weren’t at a university like IU, we wouldn’t have access to very cool, very useful, and very expensive things like mass spectrometers and NMRs.

4) Being a chemistry grad student is not all fun. When I visited the lab on Monday, I got to sit in on Nick Mayhall’s talk entitled "Transition Metal Thermochemistry and Reactivity: Developments and Applications." Nick is a fifth-semester grad student and as such, he had to present the dreaded Fifth Semester Exam.

Meghan and several other grad students helped explain to me that the Fifth, for most people, is the most frightening part of being in grad school. At some point during the fifth semester, every grad student must present a talk to a panel of faculty members. This talk, in essence, justifies their presence in the Ph.D. program.

During the hour-long talk, the faculty asked questions about Nick’s presentation, which consisted mainly of the research he’s done over the past two years and the work he plans to do in the future. None of the faculty had any sympathy and the whole situation was, in a word, terrifying. To pile on the terror, after the talk, Nick and the faculty panel went to another private room, where the questions continued with no time limit.

But, the questions aren’t just for kicks. If the faculty think that the presenter does not meet whatever standards they have, the grad student is given a master’s degree and removed from the program.

Scary, no?

5) Working in a lab is a lot like any other job. I realize that I’ve said this several times now, but this was really the most important information I gathered from my time in the lab. Lab work is much like any other work. Zaleski’s group knows a lot more about inorganic chemistry than I ever will, but their days are neither more exciting nor more boring than mine are.

They forget to label their beakers; I forget to turn in an assignment.

They have intimidating moments, like presenting their Fifths; I have intimidating moments, like interviewing a scientist for a story.

They have busy days of doing reactions and boring days of reading papers; I have busy days of tests and meetings and boring days of reading for class.

They take time off to go to lunch together and relax; I take time off to eat dinner with a friend and have fun.

So, there it is. There is no better way to learn about lab work than to get in the lab and see it for yourself, so that’s exactly what I did. Hopefully, you will do your own time in the field at some point during your science journalism career, so that you can learn firsthand about the science we love and the people who figure it out.