Friday, July 21, 2017

Summer Reading: Henrietta Lacks

Starting this year, BURECS students who have stayed in Boston for summer internships are participating in a semi-formal book club led by grad student Donovan Dennis. Unifying this summer's selections is the theme of how STEM and research interact with social issues.

Students first jumped in with The Immortal Life of Henrietta Lacks by Rebecca Skloot. This well-received book, later adapted as a movie starring Oprah Winfrey, walks the line between memoir and nonfiction narrative as Skloot describes the history of the Lacks family. Henrietta Lacks, a poor black tobacco farmer who moved to Baltimore as a young woman, developed an aggressive form of cervical cancer. She passed away in 1951 after several months of treatment at Johns Hopkins. However, before her death, a biopsy of her tumor was taken (with dubious consent) as part of widespread national efforts to culture cells that could live outside the human body. Her cells, dubbed HeLa, were and have continued to be the most successful and hardy strain, and have contributed to enormous medical breakthroughs across a wide range of fields, including the polio vaccine, cancer treatments, and even research on the International Space Station.

Skloot follows the path of Henrietta's cells in the scientific community, but she also follows Henrietta's family, who were not aware of their mother's contributions to science for years after her death. To this day they have received no reimbursement, and are too poor to afford adequate healthcare. Skloot developed a close friendship with Henrietta's youngest daughter, Deborah, and much of the book is devoted to their combined efforts at uncovering Henrietta's story.

The book explores the complex issues of race, autonomy and consent, medical ethics, and family which arise from Henrietta's situation. Students have had the chance to discuss their own views, as well as choices made by Skloot in the way she presents the Lacks narrative. After finishing the book, they met up after work to watch the movie and discuss its similarities and differences with the book.

My own reaction to the book was overall very positive; Skloot did an excellent job of weaving together the scientific and "human interest" sides of the story to form a cohesive narrative of Henrietta's enduring significance. My only critique is that Skloot herself plays such a large role in the story, despite the focus ostensibly being the Lacks family, but I think that in this case it would have been incredibly difficult to extract herself from the book without losing some of the memorable interactions that she had with members of the Lacks family.

Next on the reading list is Spare Parts by Joshua Davis, which follows four undocumented immigrant high school students in Arizona as they build a robot for a national competition.

Saturday, July 15, 2017

The Fitzgerald Lab: Salt Marshes and Sediments

Hey y’all! I’m Carina Terry and this summer I’m working in Duncan Fitzgerald’s lab. I’m a rising sophomore in the College of Arts and Sciences. I started off as a physics major, but after a semester in the BURECS program, I decided to switch to earth and environmental sciences.

The Fitzgerald lab is a perfect internship for my major. We’re studying salt marshes; their composition, dynamics, and most importantly, how we can save them from impending sea level rise. The marsh we’re looking at now is the Great Marsh right here in New England. This marsh has a high occurrence of slump blocks – large pieces on the edge of the marsh that are slowly separated from the rest of the marsh until they reach a tipping point and cave into the tidal creek. The loss of these blocks isn’t great for the marsh, as it means the marsh is eroding even more quickly.
Tidal creek with slump blocks at high tide 
Many theories in the world of marsh studies state that erosion increases when wave power increases. This is applicable to many other cases of marsh erosion, but Professor Fitzgerald doesn’t believe high wave power is the cause of our marsh’s slump blocks. The blocks that we observe are found fairly far upstream in the tidal creek – far enough that the waves can’t get that powerful because the channel is fairly narrow. Since high wave power doesn’t seem to be the cause of the slump blocks, we have to figure out what is.
To solve this question, we test the marsh in several ways. After driving about an hour north of Boston, we park our truck and then hike out into the marsh. This hike usually takes about 10 – 20 minutes, depending on which part of the marsh we’re examining. Occasionally we have to crash our way through forest and brush, which can be a bit challenging, but it’s worth it – when we make it to our marsh site, the view is beautiful.

When we reach the tidal creek, someone has to climb down into the creek. (We have to make sure we go to the marsh at low tide, so the water is shallow enough that we can do this – we don’t want anyone to take an unpleasant swim!) After they’ve climbed down, they use a special syringe to take samples down the side of the creek bed. We do this for about 3 or 4 sites a day, then head back to the lab.

Once we’ve got the samples back in the lab, we first have to dry them for several days. When they’re dry we weigh them, which will allow us to calculate their bulk density. Then we split the samples in half and begin the rest of our analysis.
Dried marsh samples
The first half are assessed for organic content. We crush the samples up into a fine powder using a mortar and pestle, then place the crushed samples into crucibles. After weighing the crucibles to find the initial mass, we place them into the furnace. Then, at around 5 or 6 pm, one of us has to come back to turn the furnace on. The samples are burned at 550 degrees Celsius (1022 degrees Fahrenheit!) for 16 hours; we come back in the morning to turn the furnace off and let them cool, then weigh them once again. Since all the organic material was burned away in the furnace, this tells us what percentage of the sample was composed of inorganic sediments and what percentage was organic.

Mortar and pestle
The other half of the samples are analyzed for biomass. First, we use a sieve to separate the sediments from the vegetation in the sample. The vegetation is dried and then weighed by itself, to find what percent of the sample was composed of vegetation. The sediments are split in half; one portion is dried and weighed, while the other is stored in a vial for future use. Eventually, these samples will be sent to a lab in Louisiana, where the size of the sediment grains will be analyzed and recorded.

Sieves and brush
Clearly, a lot of the analysis we do is related to the mass and composition of the marsh: what percentage is inorganic, how much vegetation is present, and how big the sediment grains are. We analyze these factors because we suspect they could have a correlation to how stable the marsh is. Once we have collected all our data, we will look for trends and try to find which of these factors have the largest effect on marsh stability. Then, when we know the important factors, we can work on restoring the marsh and fortifying it against rising sea levels.

The salt marsh is an important ecosystem; it serves many functions, including sheltering young fish and insects and removing carbon from the atmosphere. It’s very important that we work to keep it from being destroyed due to climate change. And, of course, we wouldn’t want to lose this beautiful view.

Friday, July 14, 2017

Dietze Lab Internship

I’m Katie Ragosta, and this summer I’m interning with Professor Dietze and working on PEcAn, the Predictive Ecosystem Analyzer. While ecologists have collected a large amount of data, and are capable of collecting more with relative ease, that data is only useful for the kinds of large scale predictions that affect policy if we have a way to synthesize multiple data sets effectively, since no one data set will give anything close to a complete picture. Essentially, the Dietze lab aims to develop a model capable of integrating multiple data sources for more accurate predictions of the carbon cycle and biodiversity.
Screen Shot 2017-06-29 at 11.42.50 AM.png
I’m majoring in Physics and Mathematics here at BU. While it sounds like those majors might not fit perfectly with an environmentally focused project, they provide a lot of experience with systems modeling and programming, both of which are important in the Dietze lab. I took Computational Physics last semester, which gave me experience with Fortran and C. I also have a job in the physics department during the school year which uses a lot of C++, and I learned some Python in high school. The experience has definitely helped a lot with my work here, but if you don’t have much formal training and still want to work in the Dietze lab, there are lots of free resources online. The Dietze lab actually mostly uses R, which I learned some of in the first few days of the job, but what I do specifically doesn’t require much R.
The goal of PEcAn is to synthesize multiple data sources, so one of the ongoing projects in the Dietze lab is incorporating new models into ours. There’s a to-do list of pre-existing models that are being gradually added. My job is to add one called CABLE, or the Community Atmosphere Biosphere Exchange Model.
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The files for CABLE are written mostly in Fortran, which is why I was assigned this particular job. The CABLE website in that screenshot has some documentation on how you should go about building and running the model, so my first step was to read through that. Then, I got to work on trying to build it. There are two versions of CABLE, an offline version that uses its own input data and an online version that can use any input data. I’ve been focusing on the online so far. Getting the model to build involved a fairly large amount of debugging, and I actually just finished building the online version today.

Now I need to run the model as a test to make sure I built it correctly and see how it’s supposed to work. This is important because my next step will be converting CABLE to the format that PEcAn’s models are supposed to use, and we don’t want anything to get lost or changed in translation. I’ve been told that transitioning into PEcAn generally goes more smoothly than the initial stages of building the model, so I’m looking forward to that. When (or if) I get CABLE fully integrated into PEcAn, I’ll take another model from the model to-do list and repeat. Working in the Dietze lab has been a great experience, and I’m really glad to have this opportunity through BURECS.

Tuesday, July 11, 2017

A visit from the Boston Leadership Institute

Throughout the 2016-2017 academic year, our lab group hosted several groups on campus in an effort to promote STEM disciplines (and specifically climate science) to high school students. Twice in the spring we were joined by TeenSHARP chapters from Delaware and New Jersey, in addition to a visit from Boston Collegiate Charter School's entire 9th-grade class.  On Friday we welcomed another group of students, this time from the Boston Leadership Institute (BLI), to the BURECS lab for a day-long introduction to Antarctic Earth science research. The students, all of whom have expressed interest in studying STEM in college, had the opportunity to hear Dr. Marchant speak about his research before multimedia presentations in the Digital Image Analysis Lab (DIAL) and a hands-on exploration of the main lab. We thought we would share a few photos from their visit with you here on the blog.

Dr. Marchant discusses the various rock formations present in the McMurdo Dry Valleys (MDV) before the students take a virtual reality tour of the central Dry Valleys. (LAB TIP: you can do this at home by going to The system works with virtual reality headsets and on desktop computers.)

Here Drew Christ, one of the BUARG graduate students, guides the BLI students through the use of the scanning electron microscope (SEM). They were able to view ancient, preserved diatoms from the MDV at over 6000x magnification!

Olivia explains the various types of grains present in an ash sample. Under the optical microscope, it's sometimes difficult to distinguish anorthoclase crystals (the important bits) from glass fragments due to their similar translucence. These students had the opportunity to try crystal picking for themselves; some found it frustrating, but a few had the sharp eyes and steady hand necessary to be quite good at it.

Donovan discusses the methods for segregating fossilized moss fragments from the encompassing mud. The mosses are some of the last known remains of vegetation from Antarctica, and have been dated to between 14.07 and 13.85 million years old. Though delicate, several students carefully separated the mosses without breaking them--we were impressed!

Noah Conley, another BURECS summer intern in the Marchant lab, gave an overview of Martian topography for the students. Using several of the labs high-resolution screens, he helped students identify the topographical features on Mars, and shared what these features indicate with respect to ice buried beneath the surface.

All in all, a great visit from BLI--we were excited to meet so many students excited about Earth science! We look forward to seeing them again next summer.

Are you and/or your students interested in visiting the BURECS lab? Send us an e-mail at burecscience at gmail dot com or ddennis at bu dot edu.

Sunday, July 9, 2017

Fitzgerald Lab - The Great Marsh

Hi! I’m Miyu Niwa, a Biochemistry & Molecular Biology major born and raised in Tokyo.

I’ve had the great opportunity of being able to work under Dr. Duncan Fitzgerald the past month, helping investigate marsh erosion in New England and the effects of sea level rise.

The marsh, simply put, is a beautiful place. From afar, you can see the fluffy green colliding with the clear blue sky as the water shimmers at the edge. It almost looks like one of those scenery default desktop pictures you can choose from on the computer. Having lived in Boston and Tokyo, I am accustomed to the bright city lights and energetic atmosphere, so the drastic difference in this new environment highlights the peacefulness of the marsh.

But the salt marsh’s beauty does not stop there – it has multiple benefits that make it extremely valuable. Marshes filter water, provide habitat and breeding grounds for various species, and are highly productive ecosystems. More importantly, marshes act as shoreline protection, shielding the coastal areas from storms and stabilizing the shoreline with their wave dampening effect.

Professor Fitzgerald’s lab investigates the current eroding of the Great Marsh, and how the marshes are responding to climate change and the accelerating rate of sea-level rise. Specifically, he focuses on Plum Island Sound, MA and takes samples from the different rivers there (Ipswich, Rowley, Parker, Essex). For us interns, work happens both in the lab and in the field. Whatever samples collected in the field are processed in the lab, which is usually why it’s right after fieldwork days that we are busiest with work. Some of the things we analyze are the organic and inorganic/biomass content in the marsh samples.

There are different kinds of work out in the field, but this particular week, we went out to four sites to set up sediment pads along 100 meters from the water. Every 5 meters there will be sediment pads set on the ground next to the flags. Every other flag will have holes dug out for cups to be placed right underneath the surface to collect the water that runs through. When we collect them after the spring tide comes, we will run the water through a filtration process to determine the amount of organics left, as well as the total sediment content. Eventually, we will have enough data to plot a graph and map out which areas tend to have more or less sediment in the water.


The great part about working with this project is how I can experience first-hand the full process of research: collecting samples in the field, analyzing them in the lab, and then creating models to visually show the data. I get to take part in every step of the research process and see how each part affects the overall results. I never thought I would have this experience of going out into the field and collecting samples, and it has now brought in a whole new dimension to my understanding of the different kinds of research. I am excited for the rest of my internship as I learn more about the work Professor Fitzgerald does in trying to protect the Great Marsh.