Making Scientists: Hopkins Authentic Research Program in Science

written by Cathy Shufro
printed in the Spring 2017 issue of Views from the Hill

In a laboratory on the second floor of Malone Science Center, eight juniors are busy at their benches. They’re learning to wield pipettes to transfer precise amounts of liquid from one container to another. They’re learning how to harness bacteria as living factories that amplify tiny amounts of DNA into quantities large enough to analyze. They’re learning to tightly close the tops of plastic centrifuge tubes so they don’t fly open. And they are learning to fail.

On this morning in late November, for example, teacher Priscilla Encarnação informs two newly arrived boys of what went wrong overnight. “Dave and Ajay, your LB broth has gone bad!” calls out course director (and molecular biologist) Encarnação. Her voice rises above the quiet conversations of students; they are rehearsing the protocol for the day’s task, isolating DNA from E. coli bacteria. “You don’t have good sterile practice,” she tells the boys. “You have to get better at it. You guys need to clean these before the end of class,” Encarnação tells them.

Fuzzy white mold suspended in Ajay and Dave’s broth shows it is not sterile. If they were to mix that broth with agar to cultivate E. coli, they would also grow a lot of other—unwanted—bacteria.

And then something else occurs to Encarnação—a failure by the entire class: “You all left your tubes in the centrifuge last time. Good old Dr. E. took them out of the centrifuge.”

“Thank you, Dr. E!” a girl cheerfully responds. And then she and the others return to their work.

Today, the 16 juniors (in two sections) are practicing techniques used in biology, but during the yearlong elective they will also develop skills required for physics and chemistry research.

This new course is unlike any other science class at Hopkins. In a conventional science class, students learn from books and lectures, then test concepts by doing “cookbook” laboratory exercises with predictable outcomes. Here, the students are learning the hands-on techniques and then designing and carrying out original experiments. As student Helena Lyng-Olsen describes it, the class has introduced the students to “living science, not just science in a book.”

The students have already begun choosing the questions they will address. They will decide on a hypothetical answer, and design an experiment to test that hypothesis. Most likely, some of the experiments won’t work.

Failure is integral to the pedagogy, says Science Department Chair Phillip Stewart. When he designed the new program with former Head of School Barbara Riley, they named it HARPS. That stands for Hopkins Authentic Research Program in Science. “That word ‘authentic’ is really important to us,” says Stewart, taking a break from his usual routine in his office in Malone. An authentic introduction to laboratory research does not protect students from its uncertainties. “We’re trying to help the kids become comfortable with failure and unclear results,” says Stewart. “To be able to learn from those failures is what makes a good scientist.”

Along with Encarnação, who teaches basic lab science methods, two other teachers collaborate to run the course: Josh Young teaches chemistry, and Ben Taylor covers physics. Sometimes two or even all three teachers work with students simultaneously.

The three approaches to science are not as distinct as they once were: as Taylor notes, the boundaries between physics, biology, and chemistry have become increasingly porous. He cites X-ray crystallography as an example. He can teach the laws of physics that allow scientists to use X-rays to create patterns that provide information about the structure of a material. Then Encarnação and Young can show students how crystallography serves researchers in biology and chemistry.

As the students practice their new skills, the three instructors are busy tracking down summer lab internships for all 16 students. They are calling on their contacts at Yale, Quinnipiac, MIT, the University of Connecticut, and beyond—UCSF and Stanford.

When the Hopkins students arrive at those required internships, Stewart feels confident that their summer colleagues will value them for more than their skills at counting bacterial colonies in a Petri dish. The students will also understand how research works. “We want these kids trained so they can walk into the lab and actually contribute rather than being a burden,” he says. “They won’t just be cleaning glassware.”

Back in the lab, the students are using a lysis buffer to break apart the E. coli cells. The destroyed E. coli will release “foreign” DNA that the students have introduced into the bacteria that served as hosts. (They inserted that DNA so that the bacteria, as they replicated, would generate more DNA—enough that the students can now isolate it from the bacteria and analyze it.) By now the students have placed the bacteria in plastic microcentrifuge tubes and are shaking them to mix the cells with the buffer. The tubes contain a silica resin that will attract the DNA and isolate it from the cell debris.

Encarnação roams the room, pausing to watch one student and then another. She buttonholes a boy who is flipping his tube without keeping his finger on its cap. “The cap was closed,” she grants him, “but don’t trust yourself: always keep your finger on the cap. Fiducia nessuno!” she tells the class. Trust no one.

She stops beside a student pipetting buffer into a tube: “I saw that [pipette] tip actually touch the side,” she tells him. “So discard that tip. Grab a new one.” (The tip may have picked up contaminants that could spoil the buffer that others are sharing.)

Encarnação approaches lab partners Joshua Ip and Dylan Sloan. They’ve spun their test tube in a centrifuge to isolate the DNA from the fragmented bacteria cells. The tube now contains yellowish fluid (called supernatant) and a small pellet of debris. “What’s in the supernatant?” asks Encarnação. “Cell membranes,” says Dylan. “Cell membranes?” A pause. “No, DNA,” says Dylan. Encarnação sounds jubilant: “Now you’re getting it. Now you’re not robots doing what Dr. E. tells you to do. Now you’re actually getting it!”

Although most of the cours is hands-on, the students have been reading journal articles in all three fields—and with a skeptical eye. They have learned how to spot an article in which the data do not support the scientists’ claims, or in which the sample size is too small for the findings to be significant. The students have already read a physics article with fabricated data and then tracked citations of the article to examine how that fakery harmed other researchers—including teacher Ben Taylor himself when he was a physics graduate student.

At first, student Gigi Speer reports, she wasn’t confident that she would be able to understand journal articles. “Looking at a crazy graph or diagram of a cell, you might get a little freaked out,” she says. No longer: “I know now I can dissect it. I can make sense of it. That’s something I learned in this class: to use all my background.”

Department Chair Stewart has noticed that some students who don’t excel in conventional science classes have flourished in HARPS. “The straight-A student is not always the best scientist,” he says. That’s because, as Encarnação puts it, knowing something intellectually and applying it are “completely different beasts.” In the lab, she explains, “It’s really about the application of content, making practical use of what they know about scientific concepts.”

Encarnação is pushing the group to lean on her less and less. “The students say, ‘We don’t know how to do this.’ And I say, ‘Yes you do. Just figure it out.’ I give them a lot of time to sit there and just look very confused and lost, and that’s OK, because they’re learning not to just quit and ask for help.”

As student AJ Marks puts it, “She tries to lead you to the answer without giving it to you.” (She must occasionally provide answers, however, because Gigi describes their teacher as “a human textbook.”)

Much of what Encarnação teaches is how to be a good lab member. Rule one is that there’s no down time. That means no chatting, no checking phones, no glancing at homework. “There’s always something to be done. They’re very much learning that,” she says. They’re beginning to take charge of what Taylor describes as “the inglorious dirty work that must be done for science to proceed.”

Gigi has clearly assimilated that precept: “Whenever you have free time, you should be doing something,” she says. “It might be washing dishes, or something needs to be made, like an LB broth or TBE [a solution that stabilizes pH]. There’s never a time when you’re just watching other people do their experiments.”

Good citizenship requires students to follow housekeeping routines scrupulously. For some students, this is their first time washing any kind of dishes, says Encarnação, a phenomenon she finds amusing. “The thing they will most learn from me is work ethic,” she says.

Finding a director for HARP wasn’t easy. Science Chair Stewart didn’t want to hire an ordinary teacher, no matter how gifted: “We’re educators, not scientists.” He sought someone with a Ph.D. in science who had worked in a laboratory—someone who knew the culture of science firsthand and how to “talk the talk,” who had published in scientific journals, and who wanted to teach high school. “I’d get a stack of 30 résumés, and it would be amazing if two of those would meet those criteria,” he recalls. Even though the salary would be supported by an endowed gift, the person hired would earn less than they likely would in academia or industry. He heard about Encarnação through the grapevine. She was doing her postdoctoral work at Yale, had earned her doctorate in pharmacology and toxicology at the University of Connecticut, had published in science journals, and was certified to teach high school science. As part of the interview process, Encarnação presented a lesson to Hopkins ninth graders on how RNA serves as a messenger for building proteins. “I was blown away,” says Stewart.

Encarnação has a mischievous sense of humor and a no-nonsense persona, and she maintains a calm demeanor despite being the mother of infant twins. “This job is so easy for me, because it’s fun,” she says. “I get paid, which is great, but I don’t consider it work at all.”

WHEN THE PHYSICS UNIT BEGINS after winter break, Ben Taylor is immersed in constructing a new physics lab. With help from students, he is piecing together the lab’s centerpiece, a Magneto-optic Kerreffect magnetometer. Called a MOKE, the set-up detects how polarized light interacts with a magnetic medium. The magnetometer will allow the students (and Taylor) to do basic research: “I really think we’ll have papers with kids’ names on them in the Journal of Applied Physics or Applied Physics Letters,” he says.

Student Joshua Ip was thrilled when Taylor invited him to build some mounts to hold lasers. “I’ve always been interested in engineering and building, so this was an awesome opportunity for me.”

Josh sees his role in science differently since enrolling in HARPS. “This class makes me not just want to study science, but to make the breakthroughs that future students will study. And now it feels possible that not only Einstein can make these discoveries, but high school students can, too.”

Gigi Speer imagines that she enters a different world each time she comes to class: “It’s like we’re leaving Hopkins,” she says, “and we’re in a real lab.”
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