Friday, June 23, 2017

Ecological Forecasting: Reevaluating Ecology in the Face of Climate Change

By: Elias Kastritis

Mathematics and Philosophy double major

The Science of Ecological Forecasting
The field of ecology is approaching new horizons through the work and innovation done at the Dietze research group here at Boston University. The development of computational and statistical models, built with analyzing vast amounts of ecological data in mind, has recast the ecological sciences as a predictive, informative endeavor, particularly in the face of climate change and its dynamic effects on ecosystems and biological systems.

The Internship
This summer internship dives right into the process of developing and implementing ecological models through computer programming languages. I joined this internship on the basis of my experience in mathematics, computing, and the biological sciences. I enrolled in BI 303: Evolutionary Ecology as well as MA 226: Differential Equations this past Spring semester, and the interdisciplinary connections between the two classes were obvious and manifold. Dynamical mathematical models are abundantly used in ecological and biological contexts to make predictions and establish theories about ecological systems. Last Fall semester I enrolled in CS 111: Introduction to Computer Science I, where I was introduced to the Python coding language. All of these experiences have inadvertently helped prepare me for the work in the internship. In the development of computational ecological models, the Dietze lab uses the statistical computing language of R, in addition to many others. Seeking to broaden my knowledge of coding languages, and given my classroom experience, this opportunity seemed a natural fit.

As you would expect, a typical day in the lab is dedicated to coding, using the software version control platform of GitHub. Many other software components are used in developing the various ecological analyzers. One such project has been PEcAn.

Picture 1. Associate Professor Mike Dietze of the Earth and Environment Department delivers a seminar on the "emerging imperative" of ecological forecasting, which seeks to synthesize vast amounts of existing ecological data into coherent, analytical, statistical forms that can then be used to make predictions (21 June 2017).

The PEcAn Project

A large project of the Dietze lab has been PEcAn, which stands for the "Predictive Ecosystem Analyzer".

It's goals, as established by the lab, includes:

"Climate change science has witnessed an explosion in the amount and types of data that can be brought to bear on the potential responses of the terrestrial carbon cycle and biodiversity to global change. Many of the most pressing questions about global change are not necessarily limited by the need to collect new data as much as by our ability to synthesize existing data. This project specifically seeks to improve this ability. Because no one measurement provides a complete picture, multiple data sources must be integrated in a sensible manner. Process-based models represent an ideal framework for integrating these data streams because they represent multiple processes at different spatial and temporal scales in ways that capture our current understanding of the causal connections across scales and among data types. Three components are required to bridge this gap between the available data and the required level of understanding: 1) a state-of-the-art ecosystem model, 2) a workflow management system to handle the numerous streams of data, and 3) a data assimilation statistical framework in order to synthesize the data with the model."

Screenshot 1. A workflow log of various model runs on the PEcAn web interface.

Screenshot 2. A typical R Studio working environment within the PEcAn development process.

Wednesday, June 21, 2017

Antarctica and Mars

Hi! My name is Noah Conley and I am a rising sophomore in the College of Arts and Sciences (CAS) double majoring in Astrophysics and Geophysics & Planetary Science. Unlike my coworkers in BURECS who work with ancient ash, crystals, or the workings of Earth, I research Mars. My goals for this summer are to expand on the surface feature inventory for Mars, to hone my GIS skills, and to learn more about Martian topography, as that may be helpful considering my majors.

Monday, June 19, 2017

BUARG Intern: Olivia Williams

Examining volcanic crystals in the SEM

My name is Olivia Williams, and I’m interning in the BU Antarctic Research lab this summer. I’m a rising sophomore in the College of Arts and Sciences. My majors are English and Earth & Environmental Sciences, with a focus in Earth & Climate.
This wasn’t always the path of study I had in mind for myself; when I first came to BU, I intended to study journalism. I thought that the BURECS program would be the perfect opportunity to hone my communication skills while learning more about the climate--an issue about which I have always been passionate. However, in the course of my first two semesters, I realized that I enjoy creative writing and literature much more than journalism. Meanwhile, BURECS connected me with my previously-undiscovered second love: scientific research.

Wednesday, January 11, 2017

One Year Later: Reflections on my time in Antarctica

One Year Later:
Reflections on my time in Antarctica

Winter has finally arrived in Boston. People are bundled up in parkas, winter hats, thick gloves, heavy boots, and scarves, as if they were in Antarctica, not Massachusetts. They complain about Boston’s cold and windy winter months, and I can’t help but laugh.
It has now been over a year since I went on my research expedition to Antarctica. And, while I am definitely enjoying a relaxing, mundane winter break at home, the anniversary of my extraordinary trip and the onset of winter in Boston have brought to mind memories, good and bad, of my time at the bottom of the world. I have finally had a chance to reflect on those unique experiences— experiences that have changed my life in ways both subtle and profound.

There are some things about Antarctica that I don’t miss. Some experiences are so uncomfortable that, despite being part of such a remarkable adventure, they can’t be remembered with even the slightest fondness. First of all, I sacrificed most comforts that the developed world takes for granted: shower, fresh food, running water, telephone, internet, toilet, and much more. Without these amenities, my weeks in the Dry Valleys were among the harshest that I have ever experienced. (On our first day back, although I was sad to be leaving our campsite, the relief of having access to a hot shower, a hot meal, plumbing, and a mattress was ineffable.)
And of course the Antarctic temperature was brutally frigid. Our struggle to stay warm never really ended, with temperatures ranging from unbearable to just sufferable. Life in general, and geological field work in particular, is very hard when you can’t feel your face, feet, or hands. I actually got a very minor case of frostbite on my right hand. The cold wasn’t just uncomfortable, but it actually posed a health risk.
Along with the obvious physical struggle of living in Antarctica came the less expected psychological struggle. It was the first year of my life that I wasn’t home for winter break. I missed Christmas, New Year's Day, birthdays, and a wedding. Some days, a powerful feeling of homesickness set in. I missed my family, friends, and neighbors, most of whom I hadn't seen for a year. Away from cell phone towers and internet access, I couldn’t even contact them remotely. After an extremely stressful semester, it would have been great to at least hear their voices. Missing them was one of the biggest sacrifices I had to make. And now that I am home, I can appreciate just how valuable my time with loved ones really is.

Friday, July 22, 2016

BURECS and the Subtle Art of Museum Education

BURECS and the Subtle Art of Museum Education

by Morgan O'Hanlon

museum room.JPG

An exhibit highlighting New England's forests at the Harvard Museum of Natural History.

Skeletons in the Great Mammal Hall in the Harvard Museum of Natural History.

The roof of a large, red-bricked building pokes out front the top of a thick canopy only a few blocks away from famous Harvard Yard. Sunlight filters down through gaps in the leaves, glittering on the distinguished exterior. Students, teachers and other curious individuals file through the enormous front doors. Catherine Pereira, a summer intern here at the Harvard Museum of Natural History, met me outside and led me up into the museum. As this was my first time in the museum, I was immediately filled with awe when I lay my eyes upon the vast collection on display. The collection of stuffed mammals and birds and one room catch my attention with their glistening, glass eyes. In another room, display cases of artfully arranged, jaw-droppingly beautiful, jewel-colored insects. Within each room, every display told a different story. Each room had its own theme--one with skeletons and taxidermy of a vast collection of mammals and birds, another room showcased the incredible biodiversity of islands. Through each room I visited, I would stop to learn more whenever something caught my eye, taking a closer look and reading the description on succinctly written labels. I looked around and noticed other patrons doing the same, taking in information at their own speed.

Word map created by Catherine Pereira as part of her project to

survey patrons about their knowledge of Microbes, the subject

of an upcoming exhibit at the Harvard Museum of Natural History.

When I asked Pereira about how museums design their exhibits to create this experience, Pereira, a BURECS student majoring in biology education, explained a few of the projects she’s been working on. Currently, she’s surveying museum patrons in order to help the director of exhibitions create a new exhibit. This, she said, is part of a plan to gauge patron understanding of microbes so the exhibit staff has a better understanding of the public’s knowledge base. “The job of a teacher is to be able to explain concepts in an understandable, yet accurate way,” Pereira said. In the case of the microbes exhibition, Pereira discovered that patrons first think about microbes as small and dangerous causes of disease--a misconception. She said that museums are most effective at teaching when they consider these preconceptions and address them appropriately in the exhibition.

“[Teachers] also have to be able to re-explain concepts in different ways for students who don’t understand it the first time around,” she said. Unlike the classroom, museums are well-equipped to present concepts in many different ways. According to her, people can better learn when museums are designed in a way that allows patrons to be self-guided, thus creating an individualized learning experience. Pereira explained to me that this was the beauty of informal education, “visitors want to learn,” she said, “the job of an exhibit developer is to help visitors get what they want, but not force them to learn about anything they don’t want to learn.”

In order to promote this freeform learning inherent to the museum experience, a lot of thought goes into planning the exhibits so that the information is presented in a manner that doesn’t overwhelm museum visitors. “We want to allow people to make choices about their learning experience,” said Janis Sacco, the Director of Exhibitions for the Harvard Museums of Science and Culture. In order to do this, she said, “you want to make sure that your message is apparent in every single thing that you look at… it’s not just about content presentation, it’s also about mood presentation.”

View from the second floor of the Great Mammal Hall in the Harvard
Museum of Natural History. The skeleton of a whale hangs from
the ceiling over the remains of giraffes, bears, and other mammals.
Throughout the museum, this philosophy is evident. In an exhibit showcasing the biodiversity of New England's forests, I picked up a handout titled “Look, Listen, Touch,” which explained the features of the room to engage the senses of visitors through the use of audio from the woodlands, three dimensional artifacts and interactive digital kiosks. The aim is to draw a visitor in by making them feel as if they’re actually out in the wilderness while subtly presenting them with further information about their experience.

Sacco’s ultimate goal is to inspire museum visitors to discuss what they learn in the exhibits, which the museum considers to be the highest level of engagement. “When we engage in conversation, we learn the most,” she said, “if we’ve gotten them to that point, that’s the pinnacle of what they can get out of the museum experience."

When it comes to science education in the classroom, Pereira thinks that teachers could help their students by utilizing some of the methods used by exhibit developers. “Working here has given me a whole new perspective on how to teach,” she said, “if I could get students in a science classroom to feel not like they’re learning, but just to feel like they’re having fun talking about or climate, plants, or whatever the unit is at the time, that would be the ultimate goal.”

Friday, June 17, 2016

BU's High-tech Interns

Ricardo Ballesteros and Alex Theodosopoulos work on creating animations on the large screens of the BURECS media lab.
Photo by M. O'Hanlon

BU's High-tech Interns  

The stark white walls of the BURECS media lab are covered in monitorseverywhere you look, a reflection is staring back at you from the black screens. At times, they are decorated with ultra high-resolution panoramic images of Antarcticas dry valleys. Most daysand at curious times of the nightthis is where one can catch a sandy-haired, hippie-looking, vegetarian named Keith Heyward, who works as the BURECS media guru. This summer, hes hosting four of the programs students.

These students are at home inside this futuristic control center. A different gadget lies on each tablean Oculus Rift here, a drone used for aerial photography there. Despite the rooms imposing digital capacity, the students seem laid back and comfortable, a demeanor they seem to have adopted from the man in charge.

Right now, the interns are editing and adding visual aids to their TedTalks”—videos that were created by the BURECS students last fall. These 2-3 minute presentations cover short explanations of environmental topics ranging from ocean currents to solar effects on Earths climate. According to the interns, the process of creating the animations for these videos is slow because of all the minuscule details. Two of the interns working on the video, Danielle Letsche and Praveen Menon, have a five-minute conversation about the exact timing of the animation of rain falling from a cloud. In another corner of the room, Ricardo Ballesteros drags a window from a computer monitor onto a digital drawing pad while Alex Theodosopoulos tells him which of the many Illustrator tools to use.

Animation of the conveyor belt theory taken from 
Praveen Menon's video on ocean currents. 
Although Heyward initially guided them, the students took over the learning process after the first week and are now mostly self-guided. Theyve learned how to use all the software in Adobe Creative Cloud and are now easily moving between Photoshop, After Effects and other programs, competently creating animations of the scientific processes the students talked about in their videos. Concepts like the one Praveen describes in his video would be very difficult to visualize without animations, said Letsche of the usefulness of their work. In that particular video, red and blue animated arrows have been drawn on a picture of the globe in order to demonstrate the circulation of hot and cold waters across the oceans. According to the interns, visuals such as this facilitate comprehension for an audience lacking a scientific background and help to promote engagement throughout the two to three minute videos. If the videos are short and concise with lots of visuals, then they can be a really useful tool, said Theodosopoulos. The faster that we can get the point across, the more useful the videos will be to educate a general audience. Beyond educating the public about scientific phenomena, science communications tools such as these can be used to facilitate the process of scientific research. The students are excited to learn about several new technologies Heyward has been experimenting with in recent months.

Praveen Menon and Alex Theodosopoulos 
discuss the number of photographs of the rock 
that they need to take from different angles. 
Photo by M. O'Hanlon
At the moment, Heyward is preparing to photograph rocks from Antarctica in order to create high-resolution 3D models. These rocks were gathered from dozens of field missions to the Antarctic Dry Valleys. Here at BU, they are stored along with ancient Antarctic ice and volcanic ash in the basement of BUs College of Arts and Sciences in a large room known as Little Antarctica. Currently, the lack of a photographic organization system makes it difficult to locate these rock samples within the rooms labyrinthine shelving system. I want create a digital database for research use, said Heyward of this plan to photograph and catalog the rocks. Once complete, each 3D model would include a spreadsheet of its specific characteristics information like the date it was collected, an estimate of its age, mineral composition, and the GPS location from which it was collected.

In addition to creating animations, Heyward has other big plans for his interns this summer that include updating his website,, which hosts a collection of panoramic images taken in Antarctica. Heyward says that he intends to add more text to his site to make it tour-like. Although it features stunning panoramic images of the Antarctic Dry Valleys, he says it lacks the content to make sense of the images it features. Eventually, Heyward and his interns will also experiment with drones to capture images for more extensive panoramas to be featured on this website. He hopes to create a high-resolution, Google Earth-type of experience where a user can zoom in on a specific rock to examine it. Heyward thinks that this method has the potential to be used as an alternative to hiking around the vast continent of Antarctica to collect data.

The information provided by these 3D images and panoramas would be of use scientists attempting to replicate experiments done in the BURECS lab. In general, scientists methods arent well-documented, Heyward said, this has been a recent issue in the news.As a program that stresses the unity in science between research, education, and communication, BURECS has made it a goal to find solutions to problems such as this. This issue, which is becoming known as the Replication Crisis has gained recent attention in the media as a problem across all scientific fields. More than 70% of researchers have tried and failed to reproduce another scientist's experiments, and more than half have failed to reproduce their own experiments, said writer and editor, Monya Baker, for Nature Magazine in a recent story featured their website. Although less than 31% [of scientists] think that failure to reproduce published results means that the result is probably wrong, the story reports, this issue still highlights the lack of effective communication between scientists in their respective fields.

Although Heywards interns are just beginning to dip their toes into the waters of scientific media, they are well aware that the work done in BURECS has the potential to come up with innovative strategies for problem solving. As they begin work using communication technologies to aid in the education and documentation of science, they will be breaking ground in making science not only accessible, but attractive to mainstream audiences.

-Morgan O'Hanlon

This time-lapse video record by Ricardo Ballesteros displays 
the intricate set-up process for 3D modeling. 

Saturday, March 26, 2016

A Month in the Life of an Antarctic Researcher, Part 4

Thriving, Moving, and Leaving 

Although long overdue, I have finally finished my blog about my trip to Antarctica. It’s impossible to accurately describe the incredible things that I experienced and the powerful lessons that I learned in the world’s coldest, highest, driest, and windiest desert, so I have instead opted to provide a day-by-day synopsis of my expedition with Professor David Marchant and graduate student Andrew Christ.

In the future I will write more about particular experiences, but for now, here is the 4th and final entry in a 4 part “Month in the Life of an Antarctic Researcher” series.