Bennington Science Mathematics and Computing

Coral Reefs and Climate Change: How Will Reefs Survive?

Please join us at our next Science Workshop as we welcome Professor Andrea Grottoli of the School for Earth Sciences at The Ohio State University. You can access a pdf of a relevant publication here.

Science Workshop is 1:00, Friday October 7 in Dickinson 232.

Refreshments will be served.

Biology faculty member Amie McClellan and rising senior Logan Traynor have just returned from a 5-day workshop hosted by the Genomics Education partnership at Washington University in St. Louis (http://gep.wustl.edu/). Dr. Sarah Elgin, the director of the GEP program, kept them on a busy schedule of learning, primarily through hands-on training, how to use bioinformatic tools to annotate and improve regions of genome sequence.

One ultimate goal of the GEP is to demystify the apparent expression of numerous genes on the Drosophila F element, which exists in a highly condensed chromatic state.  Amie and Logan learned how to search for genes, locate introns and exons, do comparative sequence analysis amongst related species of Drosophila, and learned of the computational challenges to performing all of these tasks that thus require human eyes and intelligence.  Importantly, these experiences will feed into a new course being taught this Fall (Genome Jumpstart) in which students will actively participate in computational GEP research projects, providing an opportunity for original research and inclusion as co-authors on future collaborative publications with the GEP.

They also got the chance to tour The McDonnell Genome Institute

and enjoy some time out of their computer chairs clambering around at the City Museum (yes, they climbed all the way up into that airplane!).

When asked his thoughts on the workshop, Logan said it was “incredibly rigorous, but intensely satisfying”. Amie and Logan are both excited to implement what they’ve learned this coming Fall term in the Genome Jumpstart course!

That is right, it is maybe the most exciting time of the semester. This Friday, we will have Sciencepalooza where research from across the sciences (and math) will be on display. Put it on your calendars, and invite your friends and faculty members to the party. There will be food and lots of interesting big-time science. It is also your chance to ask poster creators questions so that you can be in the know about all the research on the walls of Dickinson next term.

When: May 29, 2014. Food: 12:00 pm, Posters: 12:30 – 2:00 pm Where: Dickinson Hall

All students at Bennington participate in internships or get similar other positions during Field Work Term (FWT) – it’s one of the distinguishing features of a Bennington education. In science, this often means that students perform experimental work at research universities, gaining skills and experiences that compliment those developed through their coursework on campus.

During FWT 2014, current graduating senior Carlos Mendez had the opportunity to do breast cancer research at The Department of Cancer Biology in the Beckman Research Institute at the City of Hope. Results from his research were just published in the journal Breast Cancer Research and Treatment. He contributed to an investigation that examined the efficacy of a novel combination of drugs on so-called triple-negative breast cancers. Results indicated that this particular drug combination could offer new targeted therapies for such breast cancers, making a strong case that clinical studies in patients should be pursued.

Read the abstract here. Congratulations, Carlos

This week we will begin a series of Advanced Work presentations by our wonderful (and soon to be graduating) Science, Math ad Computing students. This Friday, Genelle Rankin and Robin Hrynyszyn will speak about their work in Science Workshop. As a reminder, the presentations will be in Dickinson 232 fro 1-2pm.

Genelle will give a talk on her research  titled “The Cockroach Escape Response: Investigating the Effects of Alarm Pheromones on the Sensory, Motor, and Central Nervous System of the Periplaneta americana.” You may have seen a preview of this research at the science poster session last year – come hear what happened with the rest of the project!

  Robin will present a talk on his work titled “Vermont Fish Diaries: A Citizen Science App for Collecting Recreational Fishing Data in Vermont.” This is the culmination of a project combining computer science and fisheries biology. Come see what Robin has accomplished over the past year!

Dr. John getting ready to dive to the Mid-Atlantic Ridge in the Alvin Submersible

On Friday April 24, Dr. Barbara John from the University of Wyoming will present several aspects of her work at Science Workshop. Dr. John has done groundbreaking work in understanding extensional plate boundaries across the globe, and has most recently focused on investigating dynamics of slow-spreading mid-ocean ridges. Come and learn about how to conduct geologic research beneath several thousand meters of seawater, and what we are learning about Earth’s last frontier.

Dr. Rick Relyea, Professor of Biological Sciences at RPI, will present at science workshop this week, Friday, March 27 from 1:00-2:00 pm in Dickinson 232. Dr. Relyea will discuss the impact of herbicides and insecticides on aquatic communities.  How have animals in these communities responded to these stressors? Here are links to Dr. Relyea’s lab website and a paper about the evolution of pesticide resistance in amphibians.

Dov Sax

Science/Math workshop this week features Dr. Dov Sax of Brown University’s Department of Ecology and Evolutionary Biology.  He will speak at 1:00 pm, Friday 20 March, in Dickinson 232.

Eucalyptus species, native to Australia, have become highly invasive in several other parts of the world — here in the hyperdiverse native shrublands of Cape Province, South Africa (photo, Kerry Woods)

Dr. Sax’s research explores the dynamics of biodiversity at very large scales in time and space.   You can find information about his research, along with links to a long list of heavily cited publications, at his website.  While his publications address topics from the spread of disease to evolution on islands to the implications of climate change for conservation policy, his talk this Friday will focus on the core of his research program — a set of interlocking questions about species invasion and the interactions between species’ ranges and changing environments.

If you’d like to prepare some insightful questions for his seminar, I’d suggest reading some of his recent papers.  Good examples would be Early and Sax (2014) and Fridley and Sax (2014) (with Bennington alum, Jason Fridley).

Spell check seems to think Geomicrobiology isn’t a real thing. But let me tell you, after spending six weeks totally immersed in helping research little microbes interacting with different minerals, it’s a real thing. This FWT, I was in Germany interning with the Geomicrobiology department at the University of Tuebingen, each week working with a different postdoc or PhD candidate. I also attended weekly seminars in the geosciences and took a few classes studying iron oxides (all in English).

Collecting lake sediment samples for lab experiments – cold work in the German winter.

Although I wasn’t conducting my own primary research in Geomicrobiology, I learned a ton working with real-life scientists. Depending on the day and project, I regularly made chemical solutions for different media, worked in a nitrogen glovebox to prepare and conduct anoxic experiments, and used many different electrodes to test redox potential of different samples. I learned how to use some really neat instruments, like the Scanning Electron Microscope (SEM) along with X-ray Diffraction (XRD) and Energy Dispersive X-ray (EDX) imaging, Mössbauer Spectroscopy, and microscopes that detect fluorescence. The SEM uses electron diffraction to get ridiculously cool images on a very small scale—sometimes 1 nm!; the XRD and EDX probes on the SEM test for crystal structures and the chemical composition of specific spots on samples.  I was fortunate enough to be able to conduct basic tests and imaging on my own using these devices—with supervision, of course.

            I not only picked up some new hardware skills, but also learned so much about cutting-edge research on topics that really interest me.  For example, one week I was shadowing a PhD candidate studying biochar, charcoal used as a soil additive in compost, as a means to reduce greenhouse gases in the atmosphere by holding it in the wooden structures of the biochar pieces.  In particular, he was studying the nitrogen cycle and how microcosms living in the biochar ­— made from sewage slush and beach wood in different kilns—might reduce methane and nitrous oxide coming from the atmosphere, compost, and other agricultural processes. Another week, I worked with a new postdoc on microbially meditated reactions in the biogeochemical iron cycle.  We took a field trip to collect soil core samples and water from a lake in southern Germany to use as media to test the growth of iron oxidizing bacteria.  All of her work was anoxic to control for the chemical oxidization of ferrous iron. I also spent one week with a geology PhD student who is researching the effects that microbes had on Banded Iron Formations of the Precambrian Era and the “Great Oxidation Event”, which oxidized much of the ferrous iron in the environment.

            Overall, I’d say this was the most informative and educational experience I’ve had in science yet. I now can question certain scientific research and how it was conducted, as well as read science papers and visualize what the author is saying. I even became more certain of my studies in geology and it gave me ideas for my senior work in the future!

Enjoying a German treat after a hard day of science

Ljubljana street scene

What did I manage to accomplish in the seven months since spring term 2014 — my just-completed sabbatical?  Maybe talking about it will help me sort it out…  Some field work and new analyses, approaches, and results from long-term studies in Michigan old-growth forests (we’re still trying to figure out what’s going on in these systems).  Networking with forest ecologists in Europe during a Fulbright project in Slovenia and through a new consortium based in Belgium.  Plans and proposals for new projects.  There’ll be some new research results and data-graphics.  There’ll also be a little bit of travelogue; Slovenia is a tiny country with some of the most distinctive landscapes and forests in Europe (and one of its most under-rated cities).  Maybe some stories about cuisine — Slovenian (przut, pork fat, bear sausage, strange wines), Belgian (beer, chocolate, mussels), Michigander (pasties).  Students in the field in Michigan, enjoying mosquitoes.

(from Naima Starkloff and Roi Ankori-Karlinsky)

Naima measuring tree diameter

We spent FWT in the hills of Sri Lanka investigating the conservation potential of Home Gardens. This agroforestry method, used in Sri Lanka for several thousand years (yep, several thousand) mimics the structure and composition of natural forest but combines it with crops, fruit trees, etc. It’s managed by human beings, from the species selected to desired growth rates. Naima’s research (for her senior thesis, with Kerry Woods) looked at bird diversity within these forests in comparison with eucalyptus plantations (another human-managed habitat) and a preserved natural habitat. Roi did a more focused study on one bird species, the endemic and endangered Sri Lanka Wood Pigeon.

We got up with the sun and counted birds for an hour each morning. We spent the afternoons measuring trees, assessing canopy structure, and fending off cobwebs. We both had to memorize and recognize 82 different bird calls.  We ate lots of curry, hiked through some of the most beautiful tropical forests Roi had ever seen (ok, he’s never been to the tropics before), and did a lot of data entry in the mosquito-heavy evenings.

Naima’s project explores the potential for using bird diversity as an assay to measure conservation potential in human forests such as home gardens and Eucalyptus-Pine plantations, as well as in native-mixed deciduous forests. More specifically, she is testing the hypothesis that habitat/canopy complexity is a driver of avian diversity across these habitats.  Spring semester will involve analyzing these data for her senior thesis; look for it in the library, as well as in a Science Workshop presentation in May! You can read more about Naima’s work now on her tumblr.

Roi on a hot tea break in a foggy Eucalyptus-pine forest

Under the tutelage of Nireka Weeratunge, Roi played “catch the pigeon” in the afternoons. Normally a forest bird, the Sri Lanka Wood Pigeon also enjoys anthropogenic goods. It loves the home-garden’s buffet of tea trees, cinnamon leaves, fresh pepper, and the canopy cover provided by the mango trees.  Roi confirmed two nesting pairs and suspected a third, and found a nest with an egg on top of a mango tree.  Though rare and fragile, the Wood Pigeon seems to like the home-garden atmosphere, suggesting  a potential role for home-gardens in protecting this Sri Lankan endemic species. Look out for a presentation by Roi on his FWT in the first couple weeks of term!

The protein-protein interaction network generated from data collected by students in Amie McClellan’s Genetics course. The figure is from the student co-authored paper just published in The Journal of Student Research.

Science courses at Bennington College are known for providing meaningful laboratory experiences involving original student research. Amie McClellan’s Fall 2013 Genetics students got to take this one step further – their term-long research project was just published in the Journal of Student Research. The students performed a genome-wide genetic screen to determine what genes, if any, were required for yeast to grow in the presence of sodium dodecyl sulfate, an anionic detergent commonly used both in science laboratories and commercial cleaning and cleansing products, such as shampoo and toothpaste. Over the course of the term, the students identified candidate deletion strains, conducted thorough re-testing for sensitivity, performed bioinformatic analyses of their data, and designed experiments to test their findings.The resulting manuscript, which is freely available through open access, can be found here: McClellan et al JSR 2015,  or via this  link.

Congratulations to all of the student co-authors: Laura M. Ammons, Logan R. Bingham, Sarah Callery, Elizabeth Corley, Katherine A. Crowe, Jennifer K. Lipton, Carlos A. Mendez, Tessalyn Morrison, and Claudia Rallis.

Seniors Carlos Mendez and Chernoh Jalloh traveled with faculty member Amie McClellan to Northwestern University in Evanston, Illinois, where they presented a research poster on ongoing efforts in the McClellan lab to characterize a novel Hsp90 co-chaperone.  Both Carlos and Chernoh are working on aspects of the project as part of their advanced work in biology.  They had an exciting time with their  “tag team” style poster presentation and, overall, a stimulating day of science and socializing. Amie served as the session chair for the last block of talks of the day, which focused on the organismal consequences of cellular stress. In trying to sum up the experience, Carlos said “The Midwest Meeting was great fun! I had the pleasure to learn about current research in the field to help move forward our work in the lab, as well as network with professors and graduate students in order to prepare for my upcoming graduate school interviews.” Chernoh added, “The conference was a great way for me to connect what we learned in the protein biology class last term to ongoing research in the field. Virtually every project presented at the conference had a root from the topics we covered in class, so it was refreshing to see the different angles that researchers are taking to investigate concepts that we had already discussed with Amie.”  Learn more about the meeting here:  http://groups.molbiosci.northwestern.edu/morimoto/MWSM/

(posted for Amie McClellan)

Technician Abbey Killam brightened everyone’s Holidays with her Chemis-Tree. It is currently residing near the Dickinson Reading Room, so stop by and admire it if you haven’t seen it yet!

photo by Molly Forgaard

        Happy Holidays from the faculty and staff in Dickinson!

Something light but substantive for the final week of classes.

For those of you unfamiliar with his work, Philip Ball is a prolific science writer. Author of twenty science books that examine science and its contributions to, and role in, society, he also regularly writes columns for Nature, where he served as an editor for twenty years, Chemical World, and other publications. His latest book, Serving the Reich, was nominated for the 2014 Winton Prize by the Royal Society (a short video of him reading an excerpt is available here). I never need much of an excuse to use his books in my courses: Stories of the Invisible, The Bright Earth, and Life’s Matrix are just a few examples.

He just posted a fascinating piece on his blog, homunculus, about a collection of chemistry sets at the Chemical Heritage Foundation that will be the focus of an upcoming exhibition. He’s particularly interested in how these kits have changed over the years and what those changes say about society at large.

Well worth a look.

Have you ever wondered how cellular cargo gets transported from place to place along cytoskeletal networks? How vesicles travel down looooooooooooooong nerve axons to reach their destinations? How force is generated on spindle microtubules to permit chromosome movement during mitosis and meiosis? Would you be surprised to learn that “two-headed monsters” are involved???

Well, two-headed molecular motor proteins, at the least! Come hear Dr. Susan Gilbert, Professor and Head of the Department of Biological Sciences at RPI, talk at science workshop about her ongoing research on the Kinesin family of microtubule-based motor proteins.

Science Workshop:  November 7, 2014.  1 PM.  Dickinson 232.

This Friday’s Science Workshop speaker is Erik Klemetti, Assistant Professor of Geosciences at Denison University, and author of the popular Eruptions blog at Wired.

His talk, “Using Crystal Age and Compositions to Understand How Volcanoes Come Back to Life” is described as follows:

Volcanoes spend most of their existence not erupting. This doesn’t mean that there aren’t a multitude of magmatic processes going on underneath. These might include intrusions of new magma, crystallization of existing magma, magma mixing and movement of crystals through the “crystal mush” that sits under the volcano. These processes all leave their compositional and temporal signature on the crystals that form and are subsequently incorporated into the magma that does erupt. I will discuss how examination of zircon crystals in magma can help us unravel the timing and nature of events that occur between volcanic eruptions with a focus on the evolution of the Lassen Volcanic Center in California. Overall, current trace element and U-Th disequilibria age data derived from zircon suggests that an otherwise moribund magmatic system can be brought back to life (rejuvenated) by new intrusions of magmatic that are geologically ephemeral, lasting years to millennia. This conclusion means that the events that lead to the 1915 eruption at Lassen Peak unfolded rapidly before the explosive eruption, the only to occur in California in the last century.