Digging – the best way to learn science

I remember meeting Maureen Munn, PhD, for the first time, almost 20 years ago. As neighbors and mothers, we often took our six children to the beach together. Her passionate belief in letting children dig and experiment to find out about the world was obvious. Let’s just say – they got dirty. Really dirty.

Now that she has won a prize from Science magazine for designing a curriculum around digital digging in a database, I am grateful her methods brought national praise. Munn has been remarkable in discovering better and better ways to help students dig, and serving the cause of science literacy for a long time from her position as director of education outreach at the University of Washington Department of Genome Sciences.

As a scientist, she has championed the hands-on explorations that are also labeled “inquiry science.” On July 25, she and her team of collaborators were honored with an award for their curriculum about smoking behavior that lets students “dig” through survey data about smoking behavior.

She explained to the National Science Foundation that her curriculum idea grew out of genetic sequencing she did with high-school students focused on finding variation in one of many genes that might be associated with nicotine addiction. Teachers and students told her they wondered about how that might relate to behavior and addiction.

“They were very interested in learning about those topics because they did affect them,” Munn said, in an interview with the NSF.

Over a period of time, she and colleagues collected some survey data from about 300 adults who smoked regularly and others who tried it and quit. They also collected blood samples from the survey participants, purified their DNA, and typed their genomes at three regions known to be associated with smoking.  The resulting database of data became the rich material in which new students could “dig” for answers. Was one thing caused by another or just correlated? How significant were comparisons?  What numbers could they trust?

Students use the curriculum “Exploring Databases” to learn the fundamentals of statistics and the limitations of asking people survey questions.

“Part of their learning experience is recognizing the shortcomings of the study,” said Munn. “The important thing is that students are able to propose their hypothesis, to be able to say whether the data supports it and to defend their results — or to reconsider them.”

When I called her to offer congratulations, Munn said she hopes teachers across the country use the free materials at the project website. “If we have done a good job, new teachers will be able to self-learn how to use the curriculum at our website,” Munn explained. Of course, the grant that funded “Exploring Databases” expires in less than 60 days. She hopes the publicity from the award may keep teachers visiting the curriculum website, even though no new work will be done on the site itself.

“Whether using a micropipette or a database, students develop a better understanding of science if they experience the practices of scientists,” she said. That includes testing ideas, trashing what doesn’t work and finding the evidence to defend a claim.

Don’t worry too much. Munn is busy on a new project about nematodes and interactions of their genomes with the environment.

 

 

Open science: sharing salmon counts

Imagine for a moment a seagrass meadow in the mouth of a river as it rolls out to the Pacific. We have these meadows here in the Pacific Northwest, and I’ve walked in their murky shallows.

They are rich places, in the sense of full of critters. They mix different ecosystems when salty sea water backs up at high tide into the fresh river water dumping out by the gallons. They are messy places, and frequently don’t charm tourists the way beaches and waves might. But many species of fish find these waters the ideal place for babies to hide out and grow. They are dynamic nurseries.

In a similar way, the movement known as open science is an argument for a rich and messy public place where ideas mix like salt and fresh water, mixing the scientific equivalent of separate ecosystems in a way that brings fresh fertile new ideas. New ideas get nourished there, in the space between disciplines. Open science means a lot of different things. It’s too big for one story, but I want to share one fishy example of how the state of Washington is sharing science data directly with you, or anybody else.

Open science can mean helping scientists to communicate faster with each other about discoveries that have synergies. But it can also mean opening data to public scrutiny and helping policy makers to visualize complicated trends and patterns in data more easily.

Jennifer Johnson, who works for the Governor’s Salmon Recovery Office, helped create a website portal that lets you see the counts of fish from any stream or lake or river where the state does this math. Sharing data directly with the public is one element of open science – literally opening up Excel spreadsheets in ways that let the public and other scientists peer inside.

People are so excited about this, she told an audience during the Seattle Science Festival. Measuring the fish is just one part of trying to understand ecosystems. By sharing the counts, there could be discoveries about regional trends that happen faster.

Just to give an example, you can click through the stateofsalmon.wa.gov and find “adult abundance” and read how many summer steelhead have been counted in Toppenish Creek. Before this data was open and online, it was dated material printed on paper in a report issued every two years. As Johnson explained in an archived panel discussion, her team took a 150+ page report and turned it into an active portal that the public, including other scientists and elected officials, can use to get updated information and make decisions.

But just like the salt and fresh water of our seagrass meadow, Johnson sees the portal as interactive and an exchange between many communities. It doesn’t just save money for taxpayers in printing and publishing hassle of mailing paper reports.  It allows state collaborators from Snohomish to Walla Walla to send information back to the portal, and “see” the data locally or regionally any time they wish. The fish are counted by many different agencies, from tribes to state biologists. In the past, those agencies had to send their data to a central state office where this was uploaded to software. Now, qualified members of the collaboration can send their new counts directly into the portal.

“We collaborate with tribes and salmon recovery efforts all over this state…This portal allows them to contribute to the data directly and shows them all the data they might need about local areas and regions,” Johnson said.

Opening up the data has led to other collaborators “racing me to see who can get their data up first,” Johnson said. “That’s fantastic. That’s exactly what we need in salmon recovery.”

More information at this video with a panel discussion of the portal.

Next blog in series on “open science” will be profile of Seattle scientist given honor by the White House in his bid to speed medical research by throwing open data.

Decoding movie about decoding DNA

The movie about BRCA1, a mutation in a gene, is about the emotion of dread.

Annie Parker, the main character,  sees a recurring symbolic doorway, over and over, that is a visual Greek chorus reminding her of her mother’s death from cancer. Parker stands in for all of us. While the monster she fears early on is breast cancer, one can easily see the movie from a more universal view. We all dread. We all feel destined.

I saw the movie June 6th, at a special premiere showing in Seattle, the city where Mary-Claire King does her daily work uncovering more and more about genomics and how our destinies sometimes get written in our DNA. The movie is fiction, but King is portrayed in it as a determined scientist. As many already know, King spent about 16 years building the case that there was a heritable cause for breast cancer. She’s spent dozens more refining that understanding. The acronym BRCA1 is the label for the mutation that she first identified as increasing risk of both breast and ovarian cancer. Annie Parker lived most of her life not knowing about this mutation – and feeling frustrated by not knowing.

Most people leaving the theater probably tell friends the movie was about breast cancer. But I think the movie was about dread itself and about scientific curiosity.  It was about the black taste of ash in your mouth at the bedside of a friend who is dying. The movie was about nausea.  But it was also about one of the antidotes to dread – understanding.

We get to know Parker through her everyday life, making lunch for her son and married to a man who doesn’t share her curiosity about the disease that took her mother and her sister. But in part, the psychological thrill of the film comes from seeing Parker set one small idea on top of another, as if using blocks, to try to find a way to explain her disease. This tentative and frail understanding slowly helps her to face the episodes of illness.

“Annie Parker is, I think, iconic of many women that I’ve met in the course of doing this work — women who were stunned by what happened, devastated by what happened, and responded not by giving up but by learning, by becoming involved, by figuring out what had happened,” King told a reporter in a story from The Seattle Times newspaper.

Over and over, Parker fights back against dread by trying to understand. Without any medical education, she still demonstrates the scientific principles of exploration and hypothesis. She creates a strange study club with a nurse and a sympathetic doctor. The trio hold meetings where they communally try to decipher published work on breast cancer and become lifelong friends in the bargain. Parker mythologizes King when she finds out about King’s work – and writes dozens of letters asking to join the research.

The movie’s director, Steven Bernstein, managed to mine some of cancer’s vilest images for humor. Parker pukes in her son’s backpack, because he won’t open the bathroom door fast enough for her to reach the toilet. “I’ll buy you a new backpack,” she says bravely, in a lilting voice that many mother’s use to try to disguise bad news from children. He stands dumbstruck by the sight of his mom with puke drooling from her mouth. The actress Samantha Morton does a great job portraying Parker.

What emerges from this complex character study of a woman is that for her – the notion that cancer might be inherited is a liberating idea. She wants to understand the how of her own family’s suffering, and knowing the science breaks a cycle of dread.

We grow to love the fictional Parker because of her faults and foibles. We love her quirky humor and her intense loyalty to certain people – even if they don’t prove all that stable. We love the way she gets hold of an idea and won’t let go. Even if her near-obsession costs her dearly. Many times in the movie, we see the healing power of understanding. People wrestle with questions and seem to heal from answers.

As the packed audience in Seattle clapped, we knew that the real-life Anne Parker of Toronto would stand before us.

She flew in to meet Mary-Claire King,  and they embraced for a long moment.  Flashbulbs threw light on it, video cameras whirred,  and the audience wondered suddenly whether we were seeing the character from our movie step out of the frame and get emotional closure.

Three people stood on stage after the show – director Steven Bernstein, scientist Mary-Claire King and stubborn patient Anne Parker. In different ways, they all faced dread. They all faced impossible odds.  One wonders if these three share a mutation somewhere, a reason they won’t quit.

Resources:

For more information aimed at helping patients understand genetic risks in breast and ovarian cancer, the patient group FORCE provides much discussion. There is a Seattle chapter of FORCE and members attended the screening and met after the movie. At that meeting, several women shared that they know they carry the BRCA1 or BRCA2 mutation, and are glad to have a place to talk to other people facing such information.

Bioethicists regularly struggle with how information about risk influences a person’s quality of life. For more discussion of “dread” in that context, and other bioethics issues, see this compendium from Nature.

In the photo above, Anne Parker is at left, Mary-Claire King is center and Steven Bernstein is at right.