Issue 18

ELEMENTS A MAGAZINE FOR SCIENCE AT THE UNIVERSITY OF PUGET SOUND

ISSUE 18 - SPRING 2016

MADRID - ACOUSTIC ECOLOGY

DIVESTMENT - BORNEO

“The most beautiful experience we can have is the mysterious. It is the fundamental emotion that stands at the cradle of true art and true science.”

-ALBERT EINSTEIN, 1931

FROM THE EDITOR

STAFF

As this semester hurtles to a close I find myself looking back through this issue and marveling at how so much work melds into a seemingly simple product. We have spent innumerable late nights and hectic weekends writing, editing, drawing, and assembling all of the material that makes up this issue. We hope that you will enjoy the product, perhaps learn something, and hopefully be driven to continue learning about our scientific reality both on campus and in the world at large.

Blake Hessel

We have made some major changes in the structure and design of Elements this year, and these changes have offered challenges in terms of direction and execution. In creating this magazine, we have continually asked ourselves the question of whom we hope to represent and serve with the publication. We hope that the magazine offers more accessible and critically engaging content for all students, faculty, and staff on the Puget Sound campus.

Kieran O’Neil

While we have continued to offer coverage of science news on a global scale, we have also put a renewed focus on highlighting the scientific research and education that takes place on this campus every day. As our university community continues to challenge students to understand the natural world, moves forward with fossil fuel divestment and new sustainability initiatives, and works to create critically thinking and scientifically literate global citizens, Elements hopes to expand and develop as a platform and resource within this curious and critical environment.

Kaley Pomeroy

I would like to thank my staff, for their persistence and continual hard work, the various artists featured, for devoting their time and talents to this issue, and Marta Palmquist Cady for her abundant patience and faith.

Elements is always looking to offer a platform for voices and topics related to science, education, and the environment on this campus and globally. If you would be interested in working for Elements, contributing content, or sharing an idea for something you would like to read about in Elements, please reach out via elements@pugetsound. edu.

Blake Hessel

EDITOR IN CHIEF

Noah Lumbantobing DESIGN EDITOR

COPY EDITOR

Kaitlyn Finlayson ASSOCIATE EDITOR

ASSOCIATE EDITOR

Megan Reich ASSOCIATE EDITOR

Elena Wadsworth ASSOCIATE EDITOR

The production of Elements Magazine is possible due to the funding and support of the Associated Students of the University of Puget Sound. We thank ASUPS and, by extension, the student body for making this publication a reality. This magazine was printing by Digital Print Services (Kent, WA) using FSC certified paper sourced from well-managed forests, controlled sources, and recycled fiber.

Cover illustration by Allison Nasson

In this issue 6

Let’s Live Greener

10

The Art of Listening

14

Cups That Don’t Hold Water

16

CRISPR:

18

Madrid Summers

20

Borneo

24

Slater Museum of Natural History

27

Pruning the Garden of the Neurosystem

28

Oncogene Mapping

29

One Precursor at a Time

30

Building Carbon Nanotubes

32

Post-It Arithmetic and the Process of Believing

34

Saving the Sundarbans

39

The Allium

40

Real News

41

Cosmonerd

42

A Student’s Guide to Astrology

Let’s Live Greener Divestment is a moral imperative and strategic action for the future AN EDITORIAL BY MATTHEW GULICK Chances are you’ve heard the word ‘divestment’ floating around campus this year, if only because someone shouted it at you in passing. Divestment simply means ‘disinvestment’, the withdrawal of money invested in a certain asset in the hopes of influencing opinion and enacting change. While this may be a simple concept, the current divestment campaign aims to help ensure a livable future for humanity on Earth. Today’s divestment movement works to remove all investments in fossil fuels: the “Underground 200” (top 100 coal and top 100 oil & gas companies with the largest potential carbon emissions), “Dirty 15” oil companies (Exxon Mobil, PetroChina, Gazprom, etc.), and privately held hydrocarbon companies.

Divestment from fossil fuel-producing companies is an international movement with a growing presence across the nation, with efforts intensifying in cities, religious groups, and institutions of higher learning. The goal of divesting from fossil fuels is to reduce the effects of climate change from yet another angle, simultaneously condemning the environmental harm these companies cause and disavowing institutions from profiting on it.

Spearheaded by the Environmental Campus Outreach (ECO) club, the University of Puget Sound’s Divestment Campaign is receiving high levels of support across the campus community from students and faculty alike: a petition drafted by the club calls on students to back the movement with their signature, stating that those who sign find it unacceptable that the University has investments in coal and fossil fuels. It went live on September 4th; by

April 11th, 872 students, faculty, alumni, and community members already had provided their support. The petition calls on the Board of Trustees to immediately abstain from all new investments in fossil fuels and to divest all current holdings over the next five years.

The Board of Trustees determines how the school’s endowment fund is managed and where to invest the money in order to maximize the return and generate the greatest amount of money for the school. According to an email from the University administration sent to students on October 7th, the University of Puget Sound has an endowment of $323.8 million (as of July 31st, 2015), of which 12.7% is invested, directly or indirectly, in fossil fuel companies.

Indirect investment simply means that some third party like an outsourced Chief Investment Officer manages investments in the name of the Board (in the case of UPS, this is Perella Weinberg Partners). In other words, the University itself does not directly purchase shares of a company, but the money still ends up in the same place.

These investments total over $41 million. The University of Puget Sound has many admirable sustainability initiatives, but the fact remains that $41 million in dirty energy directly challenges the idea that “Loggers Live Green”. Traditionally, universities have been the bellwether of progressive change for the nation, and as such it is the duty of the institution to join other universities and organizations in divestment, denouncing the climate-destroying actions of fossil fuel companies.

The present-day divestment movement is not the first

Universities have been the bellwether of progressive change for the nation, and as such it is the duty of this institution to join other universities and organizations in divestment, denouncing the climate-destroying actions of fossil fuel companies.

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Illustration by Kyle Kolisch UNIVERSITY OF PUGET SOUND | 7

of its kind, but rather part of a larger tradition of past campaigns. The most reputable divestment campaign peaked in the 1980’s, when 156 American colleges (as well as international civil rights organizations, churches, unions, local governments, etc.) divested from companies present in South Africa in protest of apartheid. Nelson Mandela credited this divestment movement with helping to bring about apartheid’s end by pressuring the government to begin negotiations which eventually dismantled the system.2 This was a powerful stance of solidarity, and one the University of Puget Sound declined to take at that time.

As the movement garnered support, it forced the South African government to enter into negotiations because of the harm divestment was causing their economy. Furthermore, it contributed to the public’s awareness of the injustices of apartheid. In the end, divestment was one tool among many used to combat a great injustice in another nation.

This latest campaign for organizations to divest from fossil fuels began in the fall of 2013, rapidly gaining momentum across the globe. As of October 22nd, 2015, 41 universities, 54 governmental organizations, 132 faith-based groups, 118 foundations, and hundreds of individuals had pledged to divest from fossil fuels, totaling an approximate $2.6 trillion in divestment funds.3 With statistics like these, it becomes apparent that fossil fuel divestment is already making a real impact increasing momentum, and in light of its intensifying momentum, it is not difficult to believe the movement will equal or exceed the impact divestment had on apartheid. The fossil fuel divestment movement is largely powered by the accelerating and increasingly recognized effects of climate change, which are subsequently spurring a social urgency for immediate and decisive mitigation. The time is now for Puget Sound to divest; a process that takes time cannot be delayed in a world where time is running out.

A 2011 volume of papers titled “The Role of Interactions in a World Implementing Adaptation and Mitigation Solutions to Climate Change” explicitly details the scale of destruction that will be inflicted upon the environment and society if average global temperatures are to rise by only 4 degrees Celsius due to carbon emissions. It states that in such a world, limits for human adaptation would likely be exceeded, as would limits for adaptation for natural systems.4 Essentially it shows that in this scenario, society and the earth as we know it would be functionally destroyed. It also asserts

that a 2°C rise is the threshold for survivability; in this state, 50% of climate change impacts on human systems would potentially be prevented and the world’s ecosystems would, for the most part, be preserved. To clarify, this is not some “doomsday” worst-case scenario projection. This is reality. According to a 2012 World Bank report, if no further action is taken to mitigate climate change, the world is on course to warm by more than 3°C above the preindustrial climate; even if nations meet the pledges made at world climate conventions, there is still a 20% chance of exceeding 4°C by 2100.5 Humanity is digging its own grave, and this necessitates proactive change in any and every way possible, including divestment.

Of course, this does not mean all we have to do is divest, or that divestment is the greatest tool for combating climate change. One counter-argument to the movement is that it contributes to a culture of “slacktivism” where people compel others to change while they themselves do not make equally important lifestyle alterations, feeling better about themselves and claiming they have “done their part” for the world. Again, divestment is one of many methods including other sustainable practices, such as reducing reliance on dirty energy and adopting sustainable practices in daily life, and in fact they all can (and should) be adopted simultaneously. Advocating one method does not negate the practice of another.

Divestment is also critiqued because of its lack of immediate economic impact on the target. According to the way in which stocks are traded, when shares of a company are purchased, that company has already maximized their profit via that initial purchase. When the buyer in turn sells their shares, they receive the money in the transaction from whoever purchased it from them, and the original company does not see any part of that profit. Turning around and selling the already purchased stock has nothing to do with the company that initially sold it, so it may appear unclear why divestment hurts the company at all. The way this works is explained by simple supply and demand. When the movement reaches a large enough scale, the amount of stock sold rises in comparison to the demand of those who would buy it, driving the price down and lowering the value of the company. As a result, those companies will have to act in a way that redeems their image and value.

An appreciable impact of this size is admittedly unlikely since it would require a massive amount of stock to enter

The time is now for Puget Sound to divest; a process that takes time cannot be delayed in a world where time is running out.

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the market, but the apartheid campaign is an example of the principle in action.

The main impact of divestment is symbolic: stigmatizing the target industries and raising public awareness of the contention people hold with their product. In doing so, the movement attempts to shift social expectations of the fossil fuel industry to a more sustainable and responsible course of action. For a company to redeem its damaged public image, it would ideally focus more on research and development in green energy.With the fossil fuel industry, however, where the very product is the one protested, it could mean the beginning of eventual decline. The fear then is that the movement will not reach a point where it makes an appreciable impact, and that investors will have incurred potential loss for a hollow gesture. In actuality, this fear of incurring loss is unfounded. Though each trust is different, divesting (by and large) does not significantly harm the investor’s portfolio, and the data does not support the skeptics’ view that removing investments in carbon negatively affects an index tracking portfolio’s return. 6 What this boils down to is the fact that even if one does not agree with the method of divestment, there is nothing to lose by joining the movement and there is potentially much to gain.

Furthermore, there is an economic argument in favor divestment in the form of “stranded assets”, assets that prematurely lose their value due to changes in the market or society or large technological innovation. An example of a stranded asset is the devaluation of print media in an increasingly electronic age. Fossil fuels as a stranded asset refers to multiple aspects, one of which is the carbon budget, which is how much carbon world governments have deemed can be burned before a hard cut-off is enacted.

Once this point is reached, humanity ideally will burn no more carbon, an action that will kill the fossil fuel industry.

There are multiple ways the budget could be implemented, but no matter what method is used the value of shares in these companies will fall.7 Another aspect of the stranded asset argument is that as society inevitably turns toward alternative fuel sources, the value of fossil fuels must fall as a result. Tom Steyer, who worked at Morgan Stanley and Goldman Sachs before founding the $20 billion hedge fund “Farallon Capital Management”, is an advocate of fossil fuel divestment. In a letter to the Middlebury College Board of Trustees, he writes that he has directed his team to divest themselves of fossil fuels, stating “I will have a fossil fuelfree portfolio myself – in part because I am convinced it will outperform the market”, citing the stranded asset argument.9

From a purely economic standpoint, research shows that results of climate change could cost up to $4 trillion by the year 2030 in impacts to health and food security as well as physical environmental changes.8 Considering that divesting does not result in economic loss but that holding fossil fuel stocks inevitably does over time, there is little reason to keep them in the portfolio.

Divestment is one action among many to fight climate change, a practical and symbolic stance that the University of Puget Sound needs to take. UPS, an institution committed to social responsibility, critical thinking, and global citizenship, has an obligation to ensure a better future for our planet, an impossible future if we do not act soon. There is no excuse to continue profiting from destruction of the environment, especially when there are alternative courses of action available. It is our mission to take a proactive stance for society and join in serving as an example for the rest of the nation. Puget Sound has many commendable sustainability initiatives, but there is still more we can do.

By joining the national fossil fuel divestment movement, we demonstrate our disapproval of dirty energy and contribute to its growing stigmatization. As we continue to work toward a greener future we must make use of every tool at our disposal, direct and symbolic. Now is the time to divest.

Now is the time to decide if Loggers truly Live Green.

UNIVERSITY OF PUGET SOUND | 9

the art of

LISTENING Preserving natural soundscapes in a noise-filled world

BY MEGAN REICH

Illustrations by Madeline Harris

It’s not a distant possibility - the next mass extinction could be already here.

According to the Center for Biological Diversity, a normal “background” rate of extinction varies between one and five species a year. Using fossil records and other data, scientists estimate that today species are dying off at 1,00010,000 times the background rate.

That approximates to dozens of species going extinct every single day. However, unlike previous mass extinction events, the driving force behind this dramatic loss in biodiversity is not physical processes, but human activities.

(1) Most of these activities leave a trail of evidence through their devastating visual impact - the jarring empty spaces of deforestation across the Amazon Rainforest, the homogenization of species composition through introduction of exotic and invasive species, and the sight of smog-covered cities from air pollution, to mention just a few. Yes, the earth looks a lot different than it did even a few hundred years ago. But unfortunately, the damage is reaching far beyond what we can simply see. We can also hear it. We might not always realize it, but sound also plays a fundamental role in defining the relationships between ourselves and the environments in which we live. (2) R. Murray Schafer (b. 1933), a musician, composer, and former professor at Simon Fraser University in Burnaby, BC, Canada, is known by many as the founder of the crossdisciplinary field of acoustic ecology, which studies the relationship between species and their environment as mediated through sound. (2) Schafer’s work stresses the responsibility we have in creating the composition of our acoustic environment - specifically, through the regulation and management of the noise pollution we impose on it. Schafer’s 1977 book The Tuning of The World introduced concepts and terminology that remain central to the field of acoustic ecology today. (2) Within the sounds of a landscape (the “soundscape”), there are three general categories of sounds. “Keynote” sounds are frequent or consistent sounds that form a background

against which other sounds are heard. They form the identity of a place, whether that be through the ocean waves of a coastal environment or the rainy ambience of a rainforest. “Soundmarks”, analogous to landmarks, represent sounds particularly regarded by a community.

Soundmarks encompass the most distinctive features that make a place unique, such as geysers, windtraps, and waterfalls. Finally, “sound signals” are foreground sounds intended to attract attention. For example, many animals also have evolved sounds that function as alarm signals to warn others of dangers. (3) Songbirds have call types specifically associated with predator threats. The peeping seet sound of these predator calls are heard at the relatively high frequency of 6-10 kilohertz -- right above the optimal hearing range of the raptors the little birds are evading.

Recent research in acoustic ecology and bioacoustics has revealed that many animals -- from mammals to fish -- can recognize the alarm signals of other species and will use them as important cues to their own survival. One soundmark with which many of us are familiar here in the Pacific Northwest is the call of the Black-capped Chickadee.

Its audacious chick-a-dee-dee-dee is a type of mobbing call. In a 2005 study published in the journal Science, Dr. Erick Greene and colleagues found that the frequency and number of “dees” attached to the end of the call is adjusted based on the level of threat presented by the oncoming predator; for instance, the frequency of “dees” increases as the predator approaches.The intricate syntax of the chickadee’s mobbing call is not only an attempt to ward off the predator directly but to attract aggregate attention to the threat, acting as a signal that encourages other birds to harass it until it departs. (4) Bernard Krause’s (1993) “Niche Hypothesis” is an insightful illustration of the nuance behind this inter-species communication.

When analyzing recordings of animal vocalizations from various habitats, he found the voices that called out “appeared to fit in relation to all the natural sounds in terms of frequency and rhythm.” This was visualized using acoustic spectrographic maps - graphs that plot out animal and insect vocalizations through frequency bands. Krause found that the frequency bands occupied by the individual vocalizations of one species left behind bands of little to no energy in which the vocalizations of other species could fit.

It was as if each species, in addition to occupying a physical

We might not always realize it but sound, in addition to vision, plays a fundamental and important role in defining relationships to the places we live in.

UNIVERSITY OF PUGET SOUND | 11

niche, was occupying its own “spectral niche” within the environment’s available boundaries of frequency and time.

(3) Krauses’s Niche Hypothesis is important because it reveals that in natural soundscapes, all sounds are heard distinctly from one another. Such a soundscape is termed by acoustic ecologists as a “hi-fi” soundscape. Beyond providing species with spectral niches within which they can communicate to each other and listen to others outside,, hi-fi soundscapes support survival by allowing animals to gain a sense of the physical space surrounding them. (3) This can be explained by lack of masking, which promotes the propagation of “acoustic coloration” - echoes and reverberations of sounds being absorbed and reflected from the environment’s physical surfaces (rock, trees) and weather effects (temperature, wind, humidity). (6) Noise pollution produced from human activity is essentially problematic because it can block or mask the delicate balance of spectral niches. If mating calls go unheard, for example, a species might die out.

Many recent studies have focused on the effects of anthrophony (human-produced sound) on biophony (sound produced by non-human living organisms). Similar to anthropogenically-driven habitat loss and urbanization, human-created noise has the potential create microevolutionary selection pressures on the species it impacts.

To name just a few studies, Slabbekoorn and Ripmeester (2006) propose that increased noise of urban environments selects for songbirds that have more behavioral plasticity (ability to adjust calls), while Katti and Warren (2003) have found that some birds adjust the timing of their calls and sing more often at night in urban environments.

Wollerman (1999) also has found that moderate noise can disrupt frogs from finding mates, possibly causing decreases in reproduction and population. (6) On a more general level, large-scale traffic and airplane noise can alter predator-prey relationships where sound is used by the predator to cue in prey. (6) In a 2013 study testing the effect of noise pollution on birds, Dr. Barber of Boise State built a “phantom road” alongside a Boise forest that functions as a major migration rest stop for birds traveling

south for the winter. The “road” was a half kilometer of speakers broadcasting a steady stream of automobile noise.

Barber found that when the road noise was switched on, the birds exhibited “lower overall body condition and gained significantly less weight” compared to birds that came through when the road was switched off. (4) Birds must constantly make trade-offs between eating and being aware of potential predatory dangers via alarm calls. Normally, a group of birds is able to allocate the responsibility of making alarm calls between members. Barber and her colleague Christopher McClure suggest that the presence of the road noise makes it more difficult for birds to hear both predators and each other, meaning that an individual bird must spend more time on listening and less time on feeding. (7) In light of these studies, could humanproduced noise be a potential factor driving the population declines of migratory birds worldwide? It’s a possibility that certainly can’t be turned down. But what was it that made Barber’s road noise so disastrous for the birds? Urban noise such as traffic noise is the epitome of a “lo-fi” soundscape. In the midst of the city, distinct pieces of sonic information are merged to a constant background buzz of traffic and industry, an anti-information that passes the boundary-line between “sound” and “noise.” The balanced spectral niches of hifi sound informs the listener by connecting them to the geography of their environment. Noise does the opposite, acting as an isolating force that encloses the listener into a smaller aural space. Since the Industrial Revolution, more and more unique soundscapes have fallen victim to this homogenized noise of urban traffic and industry. (2) In the early 1970s, Schafer and his colleagues at Simon Fraser University set out to document soundscape decline through the World Soundscape Project. One of their first projects was a field study of Vancouver, B.C.’s soundscape, in which researchers transform sound pressure measurements into comprehensive “isobel maps” that used contour lines to illustrate change in decibels over a given area, similar to altitude maps. (2) Acoustic ecologists have access to a number of technological tools for measuring and mapping the state of natural soundscapes as Schafer and his

Noise pollution produced from human activity is essentially problematic because it can block or mask the delicate balance of spectral niches.

The balanced spectral niches of hi-fi sound informs the listener by connecting them to the geography of their environment.

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team did, including geographic information systems (GIS), remote sensing software, and spatial metric software.

However, logistical problems persist. High resolution sounds files are large, and placing acoustic sensors across the landscape can be impractical to visit each recorder to change data storage cards and batteries. There is a need for more low-cost, field-ready microphones with wireless sensor networks and a renewable energy source to power them, such as solar power. (6) In response to Schafer’s early work in the 1960s and 70s, an increasing number of groups from both scientific and artistic fields have dedicated their work to spreading awareness about the importance of preserving acoustic ecological soundscapes. In particular, they are concerned with preventing the leaking of lo-fi noise pollution into habitats whose ecological functionality is dependent on the nuance of a unique hi-fi soundscape.

One such organization is the World Forum for Acoustic Ecology (WFAE), founded in 1993. WFAE is an international association of affiliated organizations and individuals of Europe, North America, Japan, and Australia devoted to “protecting and preserving places of quiet.” They stress the multidisciplinary nature of their work, inclusive to social, cultural, and ecological aspects of the sonic environment.

(8) Another outstanding individual in the field of acoustic ecology is sound recordist Gordon Hempton. Hempton is founder of the soundscape management project One Square Inch of Silence. Located in the Hoh Rain Forest of Olympic National Park, the location is monitored periodically to check for noise intrusions. According to the project policy, “if noise intrusions are observed then an attempt is made to identify and contact the responsible party and they are asked to voluntarily quiet down.” (9) The logic behind Hempton’s management strategy is that by protecting a single square inch of land from noise pollution, large areas of the park will benefit, as most noise intrusions - such as the passing of an airplane - impact many square miles. (9) Hempton has circled the globe three times in the past 30 years, capturing field recordings of natural environments and, with minimal post-production, has released commercial albums of these soundscapes to the public.

Hempton’s work has exposed the public to an aesthetic, poetic way of appreciating Earth’s sounds. For Hempton, hearing a place isn’t about listening for sound (what he calls “controlled impairment”), but simply taking it all in without expectation or bias. Take the sound of a Sitka Spruce log on Rialto Beach in Forks, WA. When the wood fibers are excited by acoustic energy the fibers actually vibrate – nature’s largest violin. Hempton emphasizes that

when we can appreciate the subtle art of hi-fi listening in a lo-fi world, we discover that “some of the most sublime symphonies have been hidden away in something as simple as a driftwood log.” (10) Like conservation biology, acoustic ecology occupies a difficult but crucial position as a values-based field. Behind both Schafer’s and Hempton’s language lies the important notion that sounds have the ability to express the identity of both natural environments and the community of organisms living in that environment.

Natural soundscapes are an endangered resource.

(10) The success of acoustic ecology management lies in our ability to understand the benefits, values, and threats that unique hi-fi soundscapes provide,

not only to ecosystem health, but to human services - cultural, historical, recreational, aesthetic, and therapeutic. By improving our relationship with nature’s soundscapes, we can enhance our ability to appreciate, manage and conserve the habitats and species that construct them. (6) And that’s where I encourage you to begin. Simply step outside and listen. Allow yourself to be present in this world. Hear yourself contribute through your breath, the rhythm of your steps on the pavement, the rustle of your clothes. You are as connected to this world as all other creatures on this planet.

UNIVERSITY OF PUGET SOUND | 13

Cups That Don’t Hold Water The biophysics of rain-driven seed dispersal in local plant species camera to analyze his results that recorded at 15,000 frames per second. Joel first analyzed how the presence of seeds affects Under the direction of biophysics program chair Rachel dispersal distance, splash velocity, and Pepper, senior physics student Joel Eklof conducted his splash angle by conducting trials with and summer research on how the characteristics of seeds without seeds. He then analyzed how four affected the dispersal of splash cup plants. Splash cup different species of seeds affected dispersal plants are stemmed plants that utilize splash dispersal to distance, splash velocity, and splash angle. give their offspring a higher probability of survival. Splash What Joel found was that the splash velocity cup plants are unique in that they use stored and released with seeds results in a reduction of splash angle, energy; they spread their seeds through raindrops. Upon average splash velocity, and average maximum dispersal striking the seed-bearing plant, a raindrop splashes up and distance. Further, different seeds with the same mass yielded very different splash angles. Overall, the addition of seeds negatively affected splash The unripe cup effectiveness and changed the splash seeds of this characteristics. Therefore, Joel came to the Marchantia conclusion that seeds do make a difference in are visisble splash cup effectiveness. Future research topics in the splash include investigating why different seeds with cup seen here; the same mass have different effects on splash. the specimens Joel also wants to investigate what specific seed seen here were characteristics (shape, size, quantity, surface, collected right density, and hydrophobicity) have on splash outside Harned plants and their seed dispersal.

Hall. Photo: We asked Joel to share some additional Blake Hessel information on his experience this summer at Puget Sound as a research student working under Dr. Rachel Pepper.

BY KALEY POMEROY

out, carrying the plant’s seeds away from the fruit body.

In his experiment, Joel investigated whether or not seeds changed the splash of splash cup plants. He also researched how different seed properties had any effect on the splash.

Joel used seeds from splash plants that he found locally, including two different species of liverworts that he found on the Puget Sound campus, Lunularia cruciata and Marchantia polymorpha. Joel used a 3D printer using CAD software to make artificial plant bodies in which the seeds reside. To mimic how a raindrop would fall on the splash cup plants in the lab, Joel used a syringe filled with water that was suspended approximately 3.46 meters high above the splash plants. Based on past research on splash plants, it is known that a 40 degree angle optimizes splash cup dispersal. He filmed the experiment with a high speed

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Q: Why were you interested in specifically studying splash plants? How does this research fit into the biophysics program here at Puget Sound?

A: “My plan is to pursue environmental engineering graduate school. My goal with summer research was to find a project that utilized my physics specialty with my future engineering plans. Splash cup plants gave me the unique opportunity to mix botany, fluid dynamics, projectile motion, and the opportunity to play with wonderful expensive toys. Going in, I knew absolutely nothing about splash cup plants, but I took biophysics with Rachel Pepper and absolutely loved it, especially the sections that concerned fluid dynamics. Working with Rachel gave me

research and development work long term.”

Q3: What challenges did you come across while working to study these splash dynamics? Did these challenges change the path of your research? How did you work through them?

ABOVE: A fully mature Marchantia, seen with various splash cups of various sizes. The entire plant shown is approximately 5 cm in diameter.

Photo: Blake Hessel

the opportunity to bridge the gap between more traditional physics, and my love of the environment and the outdoors. This is only the second year that Rachel has been at Puget Sound, and only the second year that biophysics has been offered as a course. I look forward to seeing biophysics grow at Puget Sound so that one day there may be an advanced biophysics class, a fluid mechanics class, and one day, maybe even a biophysics major.”

A3: My splash cup project was built from the ground up, so there were many challenges that were faced. In addition, much of the summer was spent simply getting the materials to conduct the experiments and build up the lab. The first challenge was building the a splash tower in which the drop the droplets from. We (Garret Buffington, and I) designed a 3.46m tower that goes all of the way up into the ceiling. Bob Peaslee, the shop specialist, built the tower design, and did all the welding in house which saved us a massive amount of money and time, he was incredible.

In addition, in the botany realm, I was absolutely upstream without a paddle. Betsy Kirkpatrick took me all around the area and gave me Botany 101 lessons where she showed me how to harvest seeds from fruit bodies, and characterize seeds by their characteristics. I had to teach myself how to 3D model, which was a frustrating, absolutely gratifying. I think I could go on forever, because the entire summer was characterized by challenges and guess and check solutions to get past them. I love problem-solving, and each day was packed full of it!”

Q: How was your overall experience as a summer research student?

A: “My experience as a research student absolutely reaffirmed my plans for the long-term future. There were amazing moments such as when my 3D models arrived in the mail, the first time seeing one of the splashes in slow motion, and getting the opportunity to make both a poster and oral presentation. There were also some very rough and scary moments such as dropping the $50,000 fast camera (whoops, luckily was okay!), thinking I took hours of data without pressing the record button, and problem-solving for days to make a drop from 3.5m high hit a 5mm cup.

Each experience reinforced the idea that I would love to do

ABOVE: One of the cup models used by Joel; three sizes of model cups reflected natural variation in cup size and allowed for precise control.

Photo: Blake Hessel

UNIVERSITY OF PUGET SOUND | 15

CRISPR:

The new reality of precision gene editing

BY NICK LYON Clustered regularly interspaced short palindromic repeats (CRISPR) were first discovered in 1987, though the full significance of this discovery has only recently become a popular subject of genetics research. (1) CRISPR is a defense mechanism by which a bacterium can survive attacks by bacteriophages,viruses that attack bacteria.(1) CRISPR sequences are short repeated segments of bacterial DNA broken up by unique sequences known as spacers.

These spacers are complementary (pair up with) segments of bacteriophage DNA. It is this quality that proves critical to CRISPR’s function as a source of adaptive immunity.

(1) When a bacterium successfully destroys a would-be viral invader, it removes a segment of its genetic code and puts it between two repeats of a CRISPR sequence.

(1) With the onset of a bacteriophage attack, CRISPR is transcribed from DNA into RNA. In these cases, the RNA segment contained between the direct repeats is sliced out by enzyme activity and forms a complex with Cas proteins (“CRISPR associated” proteins). (1) This complex finds the complementary segment of viral DNA, binds with it, and induces causes a double- stranded break to occur on either side of the sequence, thus removing a portion of genetic material critical to the bacteriophage’s viral invasion. (1) The programmable nature of CRISPR gives it an applicability far beyond conjectural curiosity. (2) CRISPR’s gene-silencing ability is so specific that modifications to the guide sequence in laboratory experiments by single

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bases failed to silence target genes. (2) Several lab studies have explored this specificity further. Tests of CRISPR’s ability to modify specific segments of DNA in human and mouse cells, for example, have found that CRISPR is capable of silencing genes within those cells without producing mutations in future daughter cells. (2) In addition to silencing genes,researchers have also begun to have success with insertion of new genetic material via CRISPR. (2) By supplying a desired segment of DNA with the programmed CRISPR sequence, the target gene is excised. Natural repair enzymes, sensing a break in the DNA, lock the supplied gene into place. (2) Furthermore, a single CRISPR/Cas system can be programmed to target multiple genes at the same time. (2,3) In this way, theoretically any gene can be silenced and replaced within that cell’s lifetime. (2) CRISPR also allows for the possibility of eliminating critical genetic information for cellular processes or passing on new genetic flaws through reproduction. Even current primary literature by professional geneticists is abound with rare words such as “exciting” to describe the possibilities of CRISPR in terms of both research and application. (2) There is a lot we do know about DNA and its regulation in cells, but there is even more that we are still working towards understanding. Both the law and the ethics of CRISPR and its uses are years behind the body of research available today, and this should be cause for caution on the part of the researchers so gleefully pushing forward.

PICTURED:

The CAS9 protein, structure depicted here, is a fundamental component that allows for the precise base pair editing of double-stranded DNA. Photo: Wikimedia Commons

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Madrid

Summers

BY ELENA WADSWORTH AND KIERAN O’NEIL The UPS Madrid Summers Program offers students studying biology, chemistry, physics, and neuroscience the opportunity to spend a summer in Madrid, Spain working in research internships at science-based companies, research centers, and universities through the Consejo Superior de Investigaciones Cientificas (Spanish National Research Council, CSIC) and Madrid Network. The application process is extensive and extremely competitive, with only a handful of students selected per year. The Program prides itself on the highly-individualized student placement process, which matches the student’s strengths and research interests to research teams in Madrid and helps foster a relationship between students and supervisors prior to the summer internship. This personalized support ensures optimal levels of success and comfort for both interns and their research teams. While some level of Spanish proficiency is required, a benefit of the program is the dual use of both Spanish and English - the two most spoken global languages - in a laboratory setting. Additionally, a 60 hour Spanish-speaking module and sixteen-hour intercultural communication seminar are offered prior to the internship to help students become more familiar with Spanish language and culture and prepare them for the challenges of working in an inter-linguistic lab.

Carsen Nies and Cheyenne Dewey were among six students to be selected for the UPS Madrid Summers Program in 2015. We asked them a few questions about their research, working in an international lab, and living in Madrid.

the CSIC with esteemed researchers on some very important research projects, my supervisors and the women with whom I worked were all incredibly warm and welcoming.

Cheyenne: I interned at Universidad Complutense de Madrid, the largest and oldest university in Spain. I worked in the Facultad de Farmacía, the pharmacy school, in the microbiology wing unit 2 on a new project the lab was starting on Candida albicans. The group was trying to see if the CRISPR method could be used to genetically engineer the yeast to prevent its pathogenicity in the human and mouse gut. There were several other projects happening in the lab at the same time, but I primarily worked on that one.

Overall, I think research work in Spain is pretty similar to that in the U.S. or other European countries. The major procedures are the same, as standard sterility and other procedures to be replicated, they kind of have to be. Many of the kits and materials I used were from U.S. manufacturers. I half expected all the work to be conducted in English, which is sort of true but also not. All of the scientists I worked with could speak pretty fluent English and their publications were in English, but day-to-day work was entirely in Spanish (except for technical terms that could not be translated). So, I got the amazing opportunity to learn microbiology research in Spanish! I had a rule with the principle investigator, Jesús Plá, the older gentleman in the photos, that I only spoke Spanish with him and he only spoke English with me so that we could each practice the other’s language.

Did you notice differences between how scientific work is approached in Spain compared to in the US?

Tell us a bit about your experiences working as research interns in Spain:

Carsen: Science culture in Spain, at least in my lab, was very different from anything I’ve ever experienced here. In particular, it was surprising to me how relaxed my supervisors and colleagues were in the lab: in the US, we often take general safety precautions by wearing close-toed shoes, wearing gloves, and wearing safety goggles when working in a labs with chemicals. In my lab, however, we were able to wear any shoe type, rarely wore gloves, and never wore goggles. Despite this lack of safety measurements, our lab was very relaxed in a good way- our work environment was far from stress-inducing, and there definitely seemed to be a high level of happiness amongst my colleagues.

Carsen: Having the opportunity to conduct biotechnological research in Spain was one I never thought I’d get to have.

Although at first it was very intimidating to be working at

Cheyenne: The science culture was very open and full of communication. I don’t know if that is different from similar large public/university laboratories because the only

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other lab experience I have had is at Puget Sound. It BELOW: Cheyenne takes a was nice to see how much break from lab work to take collaboration happened a pic with her labmates. among the ten or so units in Photo: Cheyenne Dewey the microbiology facilities BOTTOM: Carsen can be I was working in. Everyone seen here using Spanish was interested in what the style beaker and volumetric various professors, Ph.D.s, flask. Photo: Carsen Nies and interns were working on or studying. Probably

the biggest difference in culture was the Spanish relaxed nature of it all. There were still procedures that are time sensitive of course, but things were easily planned around lunch taking an hour to an hour and a half rather than rushing to get back to work.

Did the language barrier pose a challenge for you while in the lab environment and working in highly-specific fields?

Carsen: I didn’t often find the language barrier to be a challenge, as I know a decent amount of Spanish. The only challenge I ran into was understanding and using scientific terms and equipment in Spanish. Overall, though, I enjoyed working in Spanish as it helped me develop my speaking skills and I found that it was a great learning experience to conduct scientific research in a foreign language.

Cheyenne: Language was definitely a challenge, both in the lab and outside. Lab technical terms were pretty straightforward because they were derived from English, but instructions were hard to decipher at times and made my supervisor pretty frustrated when I didn’t understand what needed to be done. That was the only point of tension between my supervisor and me. Once I understood fully what needed to be done, everything turned out ok, but until that point it could be rough when she was in an off mood and I was flustered not understand her instruction. When she couldn’t take it anymore, she would switch to describing what she wanted in English, which upset me because I was trying very hard to keep up in Spanish and I knew she was catering to me.

Did your lab take break for a siesta during the day?

Carsen: In lab, we would take a coffee break around 11 am every day that lasted for 20 minutes or so, and then take an hour-long lunch break around 2 pm. We didn’t have siesta breaks, but the time we took for coffee and lunch was a significant amount.

Cheyenne: My lab did not take a break for siesta. Everyone did not leave work until the end of the day, sometime between 4 and 6 pm (starting around 9). We all took decently long lunch breaks, however, and the professors often took morning coffee/smoke breaks while the interns continued working. I think this is a good example of how lab work stays pretty consistent with other Western cultures instead of typical Spanish culture. (CONT: pg. 23)

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BORNEO

BY KIERAN O’NEIL

As students in Peter Wimberger’s “Biodiversity and Conservation in Borneo” class, we had the opportunity to dip our toes – quite literally – in the field of environmental assessment and policymaking last summer when we traveled to Malaysian Borneo (Sarawak) as part of a field course funded by the Luce Foundation. Few of us had visited Southeast Asia previously, many of us had never even set foot abroad, and nearly all of us could not have identified Borneo on a map prior to taking the course.

So when we found ourselves quite suddenly trekking through dense dipterocarp rainforests, snorkeling over clownfish-infested coral reefs, and paddling/swimming up the long tendrils of the Batang Ai River, we knew we had thrown ourselves far beyond the reaches of the Thompson lecture halls. And what a place to throw ourselves into.

Counter to its relative geographical obscurity within the Western consciousness, the Southeast Asian island

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of Borneo is the third largest in the world and accounts for no less than 6% of the world’s biodiversity, rendering it an ecological hotspot. (1) Nestled amidst the columnar dipterocarps rainforests, sprawling Sunda Shelf mangroves, waterlogged peat swamps, and high alpine meadows reside 15,000 species of flowering plants, 3,000 species of trees, and 440 freshwater fish, 420 bird, and 221 terrestrial mammal species. (2) Many of these species are endemic, such as the Bornean orangutan, Sumatran rhino, giant pitcher plant, and death-scented Rafflesia corpse flower.

These diverse ecoregions, species richness, and high ecological productivity also foster the livelihoods of the 11 million Bornean residents and one million indigenous Dayak people who have been dwelling on the island for millennia. (3) However, the very biodiversity that defines Borneo’s ecological landscape also is becoming increasingly threatened by a host of anthropogenic infringements and interventions, many of which formed the subjects of our respective studies during our time in Sarawak. In particular, unregulated logging of Bornean timber and the widespread planting of oil palm in cleared areas has resulted in the wholesale deforestation and fragmentation of critical

ecological habitat through the elimination of wildlife BELOW: Students observing a palm oil tree at a plantation corridors and substantial reductions in forest biomass. in Telok Sarabang. Oil palm is one of Borneo’s primary export (3) Throughout our travels, we observed fields upon products; consequently, its production is one of the greatest fields of oil palm planted in rows, evidence of its drivers of deforestation in the region. To date, plantations have growing demand as vegetable oil and fats in global have replaced over 6 million ha of secondary forest and critical markets. Additionally, oil palm plantations may bush habitat across Borneo. Photo: Kieran O’neil facilitate the building of in-roads connecting them to processing plants; in the village Telok Serabang, we observed oil palm being strategically planted as a front for deforestation and development projects in the area.

Additionally, the implementation of large hydropower projects along rivers has resulted in the displacement of indigenous communities and the disruption of ecological processes, as in the case of the Batang Ai River and Iban communities living upriver. When we stayed with one of the only families who refused to be relocated to the more urban resettlement zones that had been allocated for river communities, they expressed a strong resolution to maintain their livelihood in the same place they had for generations prior: living alongside the wild orangutans they considered under their care and protection.

The unregulated poaching and harvest of native species in Borneo also is of increasing concern with regards to the health and survival of many endemic floral and faunal populations, especially when compounded by the devastating effects of deforestation, land conversion, climate change, oil palm proliferation, and dams. (1) Currently, 9 of the 10 most endangered species globally dwell in Southeast Asia: the Asian tiger, Sumatran pygmy elephant, Sumatran rhino, pangolin, Bornean orangutan, sun bear, Asian yew tree, yellow-crested cockatoo, humphead wrasse, and pig-nosed turtle - and all of them highly valued for their skins, fur, claws, teeth, skulls, shells, taste, medicinal uses, or exotic domestic value. (4) The illicit harvest of animal body parts such as rhinoceros horn and pangolin scales (both of which are used as ingredients in the production of Traditional Chinese Medicines (TCMs) has driven the Bornean populations of both ABOVE: Oriental dwarf species to near-extinction. (5) Due to the exposing kingfisher (Ceyx erithaca) of previously-remote habitat via deforestation, the posing during a night trek at advent of highly-sophisticated poaching technology, Mulu National Park, Sarawak, and increasing demand from economically-booming Borneo. RIGHT: Black foreign markets, most of these species can no longer peppercorn grown on organic be found in their natural habitat but dwell exclusively farm at Telok Serabang. in protected national parks and animal reserves. Pepper is an economically (4,5) Throughout our travels we observed the often vital product in Sarawak, so devastating footprints of the illicit wildlife trade on much so that it is commonly Bornean wildlife, be it the drug-addicted orangutans referred to as “black gold”. held for rehabilitation in the Matang Wildlife Centre, Photos: Kieran O’Neil

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the endangered pygmy squirrels being sold for 600RM at a public market, or personal accounts by wildlife sanctuary workers of interactions with syndicate poaching gangs from South Asia.

In spite of these sometimes disheartening observations, our experience was by no means one cast in doom and gloom.

Rather, it merely provided a glimpse of the deep and complex interconnections between the ecological, cultural, social, political, and economic landscapes comprising Malaysian Borneo. Indeed, we perceived many instances of optimism, especially where these intersections were recognized and honest dialogues between different interest groups were cultivated. For instance, we were hosted by several communities and National Parks actively involved in ecotourism endeavors, incentivizing the protection of natural spaces while producing economic benefits for resident communities. Moreover, these experiences demonstrated the importance of interdisciplinary approaches to environmental issues, both within our own group and between the different voices governing conservation efforts.

The opportunity to not only learn about but utterly immerse ourselves within these and numerous other conservation issues currently threatening Borneo’s ecological landscape was invaluable to us as burgeoning naturalists, environmentalists, biologists, and sociologists. While it was enjoyable simply being in a place teeming with bizarre flora and fauna, being able to actively apply those investigative and empirical skills gleaned from years of traditional classroom knowledge was both empowering and humbling. And in the end, what we saw wasn’t nearly as important as how we perceived the system as a whole. After one wild orangutan trek (minus the orangutans), one of us remarked, “It’s okay that we didn’t see them because we knew they were there, and that’s all that matters. Actually, it’s better.”

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ABOVE: Students taking a tour of the Matang Wildlife Sanctuary in Sarawak. Photo: Jack Marshall

RIGHT:

Unidentified Bornean lizard seen on a wilderness trek at Telok Serabang Photo: Sam Hain

BELOW: Male orangutan

BOTTOM: Students listen to

at the Semenggoh Nature Preserve. Photo: Cliff Hayashi

a guide explaining oil palm agriculture during a tour of Telok Serabang. Photo: Cliff Hayashi

MADRID: Do you have a favorite moment from your internship?

Carsen: In my internship, I don’t have a particular favorite moment- I think every day had some great individual moments that made the internship so amazing. My favorite part of my time at the CSIC overall was working with three Spanish women who were employed by my supervisors. The three women were so kind and funny, and were incredibly easy to work with. Overall, my internship and time in Madrid were better experiences than I could have ever hoped for, and I am so grateful to have had this opportunity.

Cheyenne: I had a lot of great moments in the lab. Lunchtime conversations, since we ate lunch together as a lab unit (see photo), were always entertaining even if hard to keep up with sometimes.

Probably the best in-lab moment was when my supervisor and I finally got electroporation to work on my transformation experiment. Everyone was holding their breath because it’s very easy for the procedure to go wrong if the ion/water balance is incorrect and we had already failed when trying it before. Then it worked! I was excited because it showed I didn’t screw up the preparation before the electroporation, and my supervisor was excited it worked and we could keep moving forward. It was magnificent.

Is there a particular moment of culture shock or a funny moment you’d like to share?

Cheyenne: I think I have to go back to lunchtime conversations for this one. One of the craziest things my lab intern companions asked me about American culture was if I owned a gun. I was really surprised. What do you mean all Americans have guns? Apparently that’s what we’re known for abroad and I was appalled. Of course I don’t own a gun. There are areas of the country where almost everyone owns one, but right here and me?

Nope. There were so many conversations of Game of Thrones and other popular culture subjects, but that one stuck out to me the most.

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Slater Museum

Tucked away in the second floor of Thompson Hall, the Slater Museum of Natural History is one of the University of Puget Sound’s hidden gems.

BY MEGAN REICH

Tucked away in the second floor of Thompson Hall, the Slater Museum of Natural History is one of the University of Puget Sound’s hidden gems. Founded by Professor James R. Slater in 1930, the museum contains a substantial collection of plants, mammals, birds, reptiles, and amphibians used for both research and education. (1) Upon first glance, the sheer number of species and specimens in the museum may seem shocking. Every specimen, however, contributes to the museum’s aim of preserving biodiversity and exhibiting variation, which, as any BIO 112 student well knows, serves as the basis for natural selection. But these specimens aren’t just sitting there to display their beautiful biodiversity – they are constantly being researched and studied in new ways.

To explore how exactly Slater uses its specimens, and why they are important, we’ve talked to three staff and students who share their own unique perspectives and experiences with Slater Museum.

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Education Slater Museum also has an Americorps position, currently being filled by ’15 graduate Brenda Miller, the museum’s Education and Outreach Coordinator. We’ve talked to Brenda about the role of the position at the museum as well as insights she has gained with Slater’s education and outreach program: “While I am involved with docent training and organizing events such as Nights at the Museum, the main role of the AmeriCorps member at Slater is to teach the Nature in the Classroom lessons at elementary schools. The NIC lessons are a set of three lessons taught in 4th and 5th grade classes utilizing different kits of teaching specimens, as well as nature journals that we use to help the students learn how to make good observations, scientific sketches, and hypotheses. The first kit is a bit of a grab-bag of mystery

PHOTO CAPTION A female mallard wing specimen,

part of the Slater Museum of Natural History’s vast collection of plants, birds and other creatures.

Photo: Slater Museum of Natural History.

specimens (bones, shells, etc.) that the kids use to first learn about making observations and sketches and such.

The second kit, which happens to be my favorite, is a set of bird specimens which the kids will handle and learn how to draw conclusions from them based on their beak and feet morphology. The last kit is a set of mammal skulls that the kids will observe and then use dichotomous keys to figure out what animal their skull belongs to. What I think is especially cool about the lessons is how excited and absorbed the kids are - even the ones who are initially a bit grossed out! On top of that, they’re all just excited and happy to work on these lessons, even with all the work they’re doing inside their journals (a bunch of them get really pumped at the start when they find out that they get nature journals in the first place!). They always want to share their ideas about the specimens they have, and it can be really hard to reign them in to keep them focused on the task at hand. It’s especially gratifying for me to see their enthusiasm for these lessons because while I’m certainly teaching them how to develop these skills and giving them a ton of cool facts, for many of them the skills are already in place, they just haven’t tapped into them yet. Teaching the lessons is, in several ways, opening a door to these kids and allowing them to see and be excited about so much of nature that they probably had never even noticed before.

It’s an amazing experience, and one that I get to repeat with dozens of schools and hundreds of kids!”

Research Concentrating many specimens and species of a group together in one place is valuable for researchers. Until the 1970s, scientists relied primarily on morphologicallybased measurements. Alleviating the inconvenience and transience of field observations, museums served as a feasible and central place of research. But we couldn’t have ever foreseen the future developments in technology that have allowed us to extract even more valuable data from these specimens. For example, due to the development of PCR (polymerase chain reaction) technology in the 1990s, researchers were suddenly able to retrieve genetic information from just a small piece of tissue, exponentially increasing the value of extinct specimens. Specimens also

can help us understand sources and reservoirs of disease and act as monitors of environmental contaminants through stable isotope analysis. (2) Galen Dolkas, student docent, shares with us how he has used specimens for his own independent research: “My research is on the variation in owl feather structure as they relate to the bird’s anatomy and life history. I’m using a photographing microscope to photograph four remiges (flight feathers) from each wing of five owl species, positioned to give the widest variety of positions w/in each set of remiges (P10, P1, S1, and S10-12 depending on species). I’m recording the species, sex, and mass of the bird from the data the museum keeps with each specimen; from the specimen itself, I’m measuring the length of each remige, the rachis width, barb angle (angle the barbs attach at relative to the rachis), and barb density both parallel to the rachis and perpendicular to the barbs on both vanes.

Then, I’m examining how the rachis width, barb angle, and barb densities vary by species, habitat category, foraging strategy category, sex, mass, remige length, vane, and remige. By using the collection, I’ve been able to do in a few months with very little money what would take years of work and many thousands of dollars to do in the field.

My preliminary results have shown a few things: 1. Barb angle may be an equally important evolutionary response to the physical stresses of flight as barb density is. 2. Barb density has been measured parallel to the rachis, which is oblique to the barbs, and thus doesn’t control for the effects of barb angle; instead, my research indicates that barb density should be measured perpendicular to the barbs.

3. Rachis width responds strongly to different foraging strategies, but much less to different habitats. 4. The outer vane, (which is subject to more physical stress than the inner vane), shows far more significant responses than the inner vane; difference is especially prominent with barb angle. 5. Barb density responded more to different habitats than barb angle did.”

Get Inspired These days, the Slater Museum is buzzing with activity.

The museum is still actively acquiring specimens, mainly through salvage from private citizens and wildlife agents in Western Washington, as well as trading between other natural history museums across the country. Student docents run tours during the museum’s open hours weekly.

Around once a month the museum puts on a “Night at the Museum”, in which themed subsets of the collection are put on display to give the public a deeper look into the

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specimens that can be found in the museum. (1) We’ve asked Katy Papoulias, Education and Outreach Specialist, to share some of her favorites: “The Slater Museum houses about 80,000 specimens, meaning we have about 80,000 stories to tell! The majority of our collection consists of species that can be found in the Pacific Northwest, but we do have some excellent species from around the world. One of my favorite drawers in the museum is the one holding the birds-of-paradise that we have from New Guinea. Birds-of-paradise are probably best known for the extravagant plumage that males of the sexually-dimorphic species have, and you really can’t believe how fancy their feathers are until you see the specimens up-close. We also have two passenger pigeon specimens, which are an extinct species of bird from North America.

Besides their value for scientific research, having these two passenger pigeons also provides a great jumping-off point for conversations about the use of museum collections in research and conservation. My personal favorite specimen, though, is a Common Merganser collected by E.A. Kitchin in 1931. If that name sounds familiar to biology students, that’s because the Kitchin Library (the biology resource room) in Thompson Hall was named after him! Kitchin was a vertebrate biologist who donated a significant bird collection to the Slater Museum. Mergansers are fairly common birds here in Washington, so that isn’t the remarkable part of this specimen.

What makes this specimen unique is the 10 1/2 inch fish stuffed in the bird’s beak.

Kitchin attached a card to the specimen explaining that the merganser died by trying (and failing) to swallow a large perch, and perhaps to honor that effort, the merganser was prepared with the skinned and stuffed perch in its beak. Every specimen has a story!

Want to learn more? Visit http://www.pugetsound.edu/ academics/academic-resources/slater-museum/, where you can learn more about the history behind the museum, browse Slater’s collection, and check out other useful biodiversity resources. Or, better yet, drop by Thompson 295. Student docents are available for tours of the museum during open hours, 11:00am-2:00pm Wednesdays through Fridays. Even if you can’t make these times, feel free to check out the new interactive educational displays that surround the museum’s entrance.

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BELOW: In addition to housing a large physical collection, the museum also maintains image databases on bird wings and tails (such as the one seen on the previous page) and dragonflies. Curated by former Slater Museum director Dennis Paulson, the collection contains images of dragonflies taken all over the world. The image below shows a number of pairs of mating Argia emma at the edge of an Oregon pond.

Photo: Dennis Paulson, Slater Museum of Natural History.

Pruning the garden of the neurosystem

BY KAITLYN FINLAYSON Brianna Greenwood spent her summer investigating how fly neurons die. Neurodegeneration (loss of neuron function) is caused by apoptosis, a type programmed cell death caused by the early-onset alterations of mitochondrial structure in neurons. To do this, Greenwood examined a protein called Bruchpilot, which is responsible for the stabilization and function of synaptic connections in Drosophila flies. In other words, this gene helps the fly... fly. These proteins are called Bruchpilot, which translates to “crash pilot” in German, because Drosophila with a mutation in this gene often crash when trying to fly.

Greenwood examined Bruchpilot in the context of its relationship to another gene, the alpha spectrin gene, which is responsible for proper cellular scaffolding.

The gene for alpha spectrin can be knocked out (lose its function) if other genes in Drosophila produces RNA that interferes with the regular alpha spectrin RNA. Alpha spectrin knockdown has been known to disrupt regular cellular scaffolding. With this in mind, Greenwood sought to explore whether alpha spectrin knockdown has an effect on Bruchpilot localization in Drosophila.

Greenwood carried out this experiment by dissecting Drosophila third instar larval nervous and segmental musculature and fixing samples for scanning electron microscopy (SEM) and transmission electron microscopy (TEM). For those unfamiliar with the microscopy rooms on the bottom floor of Harned, SEM produces an image by scanning the specimen with a focused beam of electrons, while TEM is a technique in which a beam of electrons is transmitted through a specimen, interacting with the specimen as it passes through to create an image. The localization of Bruchpilot for normal and mutant synapses was detected by epifluorescence, in which a light source is mounted above the specimen with a monoclonal antibody specific for Bruchpilot.

At low magnification with SEM, the wild type (WT) and alpha spectrin knockdown Drosophila larvae were largely similar. At high magnification, however, Greenwood observed separation of the nerve from the muscle at the synapse for the alpha spectrin knockdown. Similarly, under TEM, the WT showed normal synapse and mitochondria while alpha spectrin knockdown showed degeneration

of neuron filament organization. Additionally, the inner membranes of the mitochondria in the mutant tissue appeared to be disorganized compared to the mitochondria of the normal tissue. This difference indicates that apoptosis was underway; the fly neurons were dying. Bruchpilot localization in alpha spectrin knockdown larvae was clearly less punctate than in WT larvae, indicating that a decrease in alpha spectrin had an effect on the localization pattern of Bruchpilot protein.

Given this discovery of Bruchpilot’s mislocalization in alpha spectrin knockdowns, Greenword suggested future research should be concentrated on determining which signaling pathway is affected by the knockdown BELOW: Scanning of alpha spectrin. She added electron micrographs that the examination of showing abnormal ankyrin, another protein neuro-muscular structure necessary for synapse compared to healthy stabilization, is a possible neuron growth (bottom). direction for future research Note the weak attachment on neurodegeneration. and reduced arborization

(branching) of the mutant. Photos: Brianna Greenwood

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Oncogene mapping:

modeling cancer-associated gene expression in fruit flies

BY KAITLYN FINLAYSON Biology student John Evans spent his summer studying the development and morphological effects of cancer on Drosophila flies. He focused this research specifically on oncogenes. Oncogenes are mutated forms of genes necessary for normal cell growth. Mutations of these genes leads to the mis-expression of proteins, which can result in a proliferation of cell growth and ultimately cancer. As such, oncogenes are often expressed at high levels in tumor cells. Whereas most normal cells undergo apoptosis (rapid cell death) at the end of their development, those infected with cancer continue to grow.

So why the flies? Drosophila melanogaster flies are highly versatile model organisms used to study cancer for several reasons.

Because of rapid reproduction and a small chromosome set, new generations of flies and genes can be observed in short amounts of time. Furthermore, D. melanogaster has simple tissues that are comparable to human epithelial cells, the cells that line the major cavities of the body and are the highest contributors to most human cancers.

But perhaps most importantly, D. Melanogaster has mobile pieces of DNA called “p-elements.�With these p-elements, researchers can mimic oncogenes through a biochemical method used to study gene expression known as the UAS/GAL4 system,.

The first part of the system, the GAL4 gene, is only present in certain areas of the subject organism. The second part of the system, the UAS or Upstream Activation Sequence, is an enhancer to which GAL4 specifically binds to activate gene transcription, allowing one to assign gene function to cells in vivo.

Evans used this very UAS/ GAL4 method to measure an overgrowth phenotype in D. melanogaster. D.

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melanogaster GSeE15 and GSeE28 lines were treated through a screen that allowed p-elements flanking a UAS element to insert randomly into chromosomes. These lines were then mated to an animal expressing GAL4 in order to express the potential oncogene-inducing phenotype.

To accomplish this, Evans used PCRto amplify the DNA and map the location of the UAS insertion. From here, Evans bred in four lines expressing GAL4 in wing tissues, eye tissue (gmrGAL4), and gut stem cells (escGAL4) were bred with the lines containing the p-element flanked UAS. From this point, Evans was able to select the flies selected for the desired phenotype. Using light microscopy and scanning electron microscopy to observe the F1 flies, Evans indeed found slight phenotypic differences between offspring coexpressing UAS/GAL4 and those that not expressing the lines. These differences were most evident when comparing the wings of GAL4 and wild-type flies; rapid and haphazard cellular growth in the mutant flies resulted in Evans suggests that future research should focus on e identifying oncogenes and discovering where, precisely, they are expressed. In particular, studies should examine protein and pathway interactions to assess how oncogenes are affected by these pathway interactions.

BELOW: Drosophila wings are commonly used to observe cell growth because their thin layers allow for easy observation of cell proliferation. Photo: Wikimedia Commons

One precursor at a time: a tricky synthesis sees some success

BY STAFF With the collaboration of Professor Luc Boisvert here at the University of Puget Sound, senior chemistry student Lisa Colombo conducted summer chemistry research on the synthesis of ligands and iron precursors. This project was part of a larger continuing endeavor by the Boisvert lab to form iron-based hydrogenation catalysts. The hydrogenation of carbonyl groups is an important catalytic reaction in the pharmaceutical industry. Current catalysts for this reaction are very efficient, but are based on iridium, rhodium, or ruthenium metal centers - which happen to be quite expensive, toxic, and scarce. Iron would be a more abundant and environmentally-friendly option, reducing both cost and hazardous waste. While iron-based catalysts do currently exist, more research is needed in order to fully explore their potential in the applied realm. Enter Lisa Colombo.

Last summer, Colombo conducted summer research in collaboration with Professor Luc Boisvert on the synthesis of ligands and iron-based precursors as part of a larger mission to form these iron-based catalysts. So how exactly does an iron-based catalyst work? In hydrogenation reactions, iron catalysts are used to break the H-H bond of dihydrogen and form Fe-H bonds. The H-H bond is usually broken through either homolytic or heterolytic cleavage.

The iron catalysts targeted in this research work through a pyridone-assisted heterolytic cleavage mechanism, which is known to be efficient for other metals, but has not been studied for iron.

For her summer research project, Colombo aimed to form five iron precursors, synthesize two ligands, and attach the ligands to the iron precursors to form the potential iron catalysts. Bipyridine was used as a the primary model ligand to test the precursor’s reactivity. Lisa succeeded in synthesizing an orange powdery that represented the first iron precursor. 1H NMR spectroscopy confirmed the identity of the product (success!). Things were a little bumpier with the second iron precursor. Trimethyl, triethyl, and triisopropyl phosphites were successfully attached, but attempts to add bipyridine, two other bipyridine-based ligands, and dppe (a common ligand in catalyst synthesis) yielded either a red solid (not the intended product) or

failed to react. Similarly, the formation of the third iron precursor was unclear. The THF complex involved in the reaction was very air-sensitive, so all attempts were impure and brown, even when a Soxhlet extractor was used for product purification. While one pathway for the fourth iron precursor appeared promising - NMR possibly showing the desired product and free bipyridine - both reactions were air sensitive and impure as well. For the fifth ligand, reactions with R=H, OMe, OH, and dppe were unsuccessful and the 1H NMR spectra were difficult to interpret. Nevertheless, Colombo broke ground in the successful synthesis of both ligands.

Colombo suggested that future work for this research should include the isolation of the first iron precursor and must achieve attachment of bipyridine, dppe, and the ligands; Colombo was confident that these steps could be achieved with sufficient manipulation of ligand-binding BELOW: Lisa hard conditions, and is excited to at work in the glove see what sorts of synthesis box, a sealed space strategies are used by future that allowed her to run research students in the reactions in an oxygenfree environment.

Boisvert lab.

Photo: Lisa colombo

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BUILDING CARBON NANOTUBES

BY KALEY POMEROY Working with Rohan Dhall, Jihan Chen, and Steve Cronin at the University of Southern California, Juliana Echternach spent her summer conducting physics research on carbon nanotubes (CNT). Carbon nanotubes are cylindrical macro-molecules of carbon -- envision a sheet of graphite being rolled into a cylinder. (1) Arranged in this way, CNTs can demonstrate outstanding electrical, optical, and mechanical properties. For instance, despite being light and flexible, CNTs are up to one hundred times stronger than stee (2) CNTs have numerous and fascinating potential applications in fields ranging from healthcare to electronics and everything in between. (3) To examine some of these characteristics and applications further, Echternach decided to start from scratch: by growing her very own carbon nanotubes.

CNTs can be grown through a process known as chemical vapor deposition (CVD). This process utilizes a recipe of gas-flows through a furnace device at different tem-

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peratures and times Part of this process involves creating pn-junction devices. pn-junctions are interfaces that form between different types of semiconductor material and are the building blocks to electronic devices such as diodes.

Echternach grew nanotubes through the CVD process and characterized them by the conductance they created (2,4) CNTs have the ability to display metallic or semiconducting properties based on the symmetry of the “twist” of the tube.

Therefore, the chirality (symmetry) of specific CNTs grown can be inferred based on its conductance. (1) Echternach also performed a “Chip-to-Chip transfer” of CNTs from transparent quartz chips with pillars to single pre-patterned electrode chips. These transfer chips are useful because they can further characterize the CNTs by measurements of photo-current, photo-voltage, Electro-Luminescense (EL), and Photo-Luminescense (PL). With Chip-to-Chip transfer Echternach was able to isolate single suspended CNT, which are difficult to grow directly. In

PHOTO CAPTION

This scanning electron micrograph shows a successfully grown nanotube. That thin white line stretching between two ends of an electrode. Photo: Juliana Echternach

OPPOSITE: Carbon nanotubes are made up of six-membered rings that form a single-layer carbon structure called graphene; the rings can have various structural traits that confer conductivity or structural integrity. Illustration

by Rory Wong Jacobs this process, the chip was glued on a glass slide, flipped and aligned to fit across an electrode. Through detecting CNTs through PL imaging SEM (scanning electron microscopy), Echternach found evidence of photocurrent and photo-voltage (70mv), simply from turning on/off lights in the lab.

(2,4) In sum, Echternach was successful in both growing CNTs and in the fabrication of devices that display either metallic or semiconducting properties with low contact resistance. The Chip-to-Chip transfers also exhibited rectifying diode-like behavior with the existence of both the photocurrent and photo-voltages. Echternach recommends that future work for the lab should involve the continuation of current studies, hopefully gathering more data on electrical and optical properties of CNTs and the devices on which they are grown. (4)

CNTs hold a number of fascinating current and potential applications in fields ranging from healthcare to electronics.

Despite being light and flexible, CNTs are very strong - up to one hundred times as strong as steel!

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Post-It Arithmetic and the Process of Believing AN EDITORIAL BY BECCA EBERT In the hallway on the third floor of Thompson, there is a poster celebrating over 900 years of achievement in mathematics. “The Men of Mathematics” poster includes the great achievements of Galileo, Gauss, Fermat, and LaGrange, among others. After a Post-It prompted the question, “Where are the women at?”, someone put fourteen Post-Its with the names of women who made contributions to mathematics. Fourteen women. In 900 years. On PostIts. The fact that women are underrepresented in math and the historical record in general should not be too shocking, but I think this fact, as a representation of how we think about who does math, illuminates a persistent habit that we often have when thinking about math. I personally believe encouraging women (and people in general) to study math requires changing the way we view the discipline itself.

Rather than focusing on getting the right answer (which is why people simultaneously love and hate math), I think we need to focus on the process of getting and believing it is the answer. Rather than looking at those very, very few people who were so skilled at getting the right answer as arbiters of who does math, and as representatives of legitimacy as

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mathematicians, we must instead find catharsis and reward through the acts of trying, and, possibly, doing.

I am a double major in Math and Comparative Politics.

In addition to wondering how my two majors fit together, people are often surprised and a bit impressed that I study math. Almost without fail, I respond, “Eh, math doesn’t make sense most of the time.” This is my way of assuaging their views that I am somehow smarter because I study math, and it is absolutely sincere. Very rarely do I feel that I understand math.

I have found that people view math as inaccessible—or at least more so than politics. I have heard countless times that someone is “just not a math person.” I think we can all think of someone—from elementary school, high school, a current class—who is just such a “math person.” I know I have had numerous classes with people who just seem to get it. They appear to take in everything the professor is saying and then ask a clarifying question that often makes me more confused and, frankly, makes me feel pretty dumb. Why don’t I understand? Am I not a “math person”?

Why is this my major?

I think these people—the people who just seem to get it— are by far and away the people most encouraged to pursue math, and rightly so. For some people, numbers make more sense, and I am confident they will apply their knowledge to some pretty amazing endeavors. I think what is most important is to ensure that these people aren’t the only ones encouraged to study math. There is the idea that math is just the way some people think, and that they don’t have to work for it. I know so many “math people” who work so hard, and I think we can’t and shouldn’t shy away from this fact. I work really hard to understand math, and a lot of times, I work really hard and conclude that math will never make sense. It certainly does not come easy to me, and for a while, I thought this meant I wasn’t a real math major. I am fairly confident that winning a Fields Medal is not in my future, but I am also positive that I am a mathematician.

Math, to me, is a way of thinking and the process of connecting and extrapolating. It is not an equals sign, it is not a word problem, and it is often not even numbers.

Math is staring at a theorem for an hour and having no idea how to prove it. Math is trying a couple (or five or eleven) approaches and hitting a dead-end. Math is finally, after

days of staring, writing “therefore” at the end of a proof.

Math, to me, is saying “I don’t believe you,” and having a professor literally prove it to you. Math is proving it for yourself. Math is not the answer but the painstaking process of getting and believing that it is the answer.

If math is just for “math people,” I am certain I would not major in it. Luckily, I have had teachers and professors who have encouraged exploration and have allowed me to pursue my ignorance rather than copy a method and recite answers. Math is a difficult process, and I think that transparent grappling with - and understanding of - this process needs to be at the forefront of the discipline. I really do believe anyone can be a “math person,” and I think we need to embrace the confusion, encourage the frustration, and celebrate the conclusions.

Although the symbolism of the Post-It is powerful—useful, temporary, easily removed and forgotten—these people represent math. It is time we recognize the numerous women who have made significant contributions to the field of mathematics. Beyond that, it is time we recognize all of the women who did not make significant constributions to math. Those who never had the opportunity to have their turn grappling with math, barred by law, institutional policy, society, or internalized discomfort with the subject.

It is time we focus on the process of math and recognize the non-“math-people” mathematicians. So, here’s to the PostIt mathematicians as well as those who really don’t believe math makes any sense but do it anyway.

Graphics by Natalie Balkam

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saving the sundarbans

Towards the Conservation of Earth’s Lungs and Ocean Nurseries

BY KIERAN O’NEIL

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Comprising the largest block of mangrove forest globally and accounting for 3% of global mangrove area, the Sundarbans of Eastern India and Bangladesh are biogeographically, ecologically, and culturally unique in their species biodiversity and ecosystem services. The Sundarbans are composed of numerous islands formed by sediment deposits by three major rivers: the Ganga, Brahmaputra, and the Meghna. (1) Subsequently, large seasonal and spatial variability in hydrological regimes foster high habitat heterogeneity and render the region prime mangrove ecosystem, providing critical habitat for nesting and migratory bird species, crocodiles, and a variety of threatened and endangered mammal species including Bengal tigers, spotted deer, fishing cats, and dolphins. (2) The Sundarbans also fulfill an increasingly critical role in primary production and carbon sequestration in the face of accumulating climate change effects.

(3) The Sundarbans support one third of Bangladesh’s population through the provision of staple food items (208 species of fish, crab, shrimp), commercial fishing opportunities, forest produce, and water quality maintenance and environmental storm control for coastal communities. (4,5) Additionally, UNESCO has recognized the Sundarbans as a World Heritage Site, indicating the cultural significance of the mangrove forest to local indigenous populations and foreign visitors alike. (5) The ecological productivity of the Sundarbans render them a vital feature of the natural and anthropological landscape of coastal Bangladesh and India, supporting a host of ecological functions and livelihoods for more than 4 million coastal peoples.

In spite of their critical biological and anthropological significance, the Sundarban mangrove forests are facing systematic decimation by the construction of shrimp ponds for largescale aquaculture projects. Given their brackish composition, convenient coastal location, and relative ease of land conversion, mangrove forests have increasingly been targeted as ideal sites for shrimp aquaculture. (6) Valued at US$9 billion and growing at 10% each year, the global shrimp industry is one of the primary drivers of mangrove deforestation and has converted approximately 1.5 million ha of coastal lowlands into shrimp ponds to date. (6) A majority of these largescale shrimp farming

endeavors are heavily concentrated in tropical lowlands of coastal South Asia, which currently account for about 75% of farmed shrimp globally. (1) Subsequently, it is estimated that over 110,000 ha of Sundarban mangrove forest have been converted to shrimp aquaculture due to regional population increase and inflated global demand for the giant tiger prawn (Panaeas mondon). (7,8) Compared to 1960s estimates, this is a 60-80% decrease in traditional mangrove forest cover. (9) The ecological and anthropological implications of this aquaculture conversion are substantial and numerous.

Shrimp farming involves the creation of ponds and enclosures to harbor juvenile shrimp until they reach harvestable size. (10) According to a recent survey of shrimp farming in the Sundarbans, a majority of aquaculture projects are labeled as “extensive”, meaning large areas of mangrove areas are enclosed by dikes to allow concentrated polyculture of shrimp. (10) These are supplemented by “intensive” and “semi-intensive” farms, which account for approximately 42% of aquaculture projects in the region and involve the construction of ponds that are artificially stocked with juvenile shrimp; these methods are particularly utilized by largescale shrimp industries and yield 5,000-20,000 kg of shrimp/ ha. (9,10) The health of mangrove trees is dependent on water and nutrient flow; therefore, even in extensive projects where mangroves are left standing, the isolation and stratification of water in farmed areas kills them after 3-5 years. (6,10) Mangrove loss has significant and adverse ecological effects, including reduction of available nursery habitat for juvenile marine species, reduced biodiversity, loss of filtering actions, soil destabilization, and reductions in primary producing, nutrient cycling, and carbon sequestering capacities. (6,10) Furthermore, waste production and pollution from shrimp ponds exert significant environmental impacts on adjacent habitats and the health of wild marine stocks . (9) These pollutants fundamentally alter the biogeochemistry of mangrove forests, inhibiting photosynthesis, respiration, and water metabolism of mangrove trees and contaminating faunal species. (9) Shrimp farming also has negative implications for food security and economic capacity of coastal populations.

The ecological productivity of the Sundarbans render them a vital feature of the natural and anthropological landscape of coastal Bangladesh and India, supporting a host of ecological functions and livelihoods for more than 4 million coastal peoples.

UNIVERSITY OF PUGET SOUND | 35

(11,12) Loss of mangrove ecosystem reduces availability of staple foods for rural and marginalized communities, many of which are already under pressure from geographic isolation, chronic poverty, and dependence on mangroves for subsistence living and supplementation of diet. (4,11) Shrimp aquaculture converts valuable nursery habitat for young fry into monocultured shrimp ponds, reducing available stocks and directly eliminating a main source of protein from the diets of coastal populations. (10) This stands to have a profound impact on the local subsistence and commercial farming. As fishing constitutes a critical source of livelihood for coastal Bangladeshi people, generating local economic growth and food provisions, limited access to fishing grounds and reduction of wild stock have devastating health and socioeconomic effects on coastal populations. (4) Prolific unemployment and displacement of coastal communities by shrimp aquaculture systems has incited interregional social conflict between fishing communities and extraction companies. (10) Removal of mangrove forests and their natural protective services also increases vulnerability of coastal communities

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ABOVE: A mangrove tree with roots exposed during low tide. Although mangroves generally grow in dense thickets, this lone tree shows the stabilizing structure of the tree’s roots within the sandy substrate. Photo: Kieran O’neil

BELOW: Mangrove forests grow in saline areas along many tropical coasts and perform important ecological and economic services, such as erosion control and acting nurseries for young fish.

Photo: Kieran O’neil

Removal of mangrove forests and their natural protective services also increases vulnerability of coastal communities to environmental disasters; indeed, tragedies such as the Indian Ocean Tsunami disaster of 2004 highlight the vital interdependence of environmental and human security.

to environmental disasters; indeed, tragedies such as the Indian Ocean Tsunami disaster of 2004 highlight the vital interdependence of environmental and human security.

(1,4) Current regulation involves federal protection designations of Sundarban forest and management strategies to keep shrimp aquaculture projects in line with these designations. The Biosphere Reserve in India recognizes three regions: a Core Zone with strict conservation measures, which includes the National Park and Tiger Zone; a Restoration Zone of degraded forest where restoration projects are currently targeted; and a Development Zone, which allow for the extraction of income-generating resources. While this management strategy involves the designation of large areas based on the integration of wildlife and community needs, Bangladesh management is characterized by protection designations of biodiverse “hotspot” areas and is managed as a refuge, creating a more fragmented protection landscape with a greater focus on species conservation. In

ABOVE: Aerial roots called pneumatophores facilitate gas sequestration from the atmosphere and nutrient absorption from the waterlogged soil. The upturned orientation of the roots allows mangrove trees to process gases even while submerged during high tide.

spite of these designations, the total areas of these sanctuaries is not sufficient to provide long-term protection to wildlife or habitat, and regulatory differences between India and Bangladesh stand to create regional disparities in preservation, possibly adversely affecting ecological contiguity. (8,9) A National Fishery Policy was enacted in 1998 to “promote and manage shrimp farming” in coastal lands, requiring cooperative selection of farming zones with the Ministry of Environment and Forests; however, almost none of these policies are being implemented. (5) Therefore, current regulations protecting the Sundarban mangrove forest are inadequate in their coverage, management, and implementation, resulting in a proliferation of paper policies that have little conservation value. (1) Several projects have been developed to enhance existing regulation and protection of the Sundarbans and increase accountability of largescale shrimp farmers. The Sundarbans Biodiversity Conservation Project was created by the Asian Development Bank in 2001 to develop alternative livelihood options and work with stakeholders to achieve

UNIVERSITY OF PUGET SOUND | 37

“long-term sustainable conservation of the biodiversity of the Sundarbans Reserve Forest through awarenessraising, training, and government support”. (13) While this increased national attention for conservation, the project lacked substantive change to habitat designations and had no implications for shrimp farming. (6) A slightly more effective initiative is the Environmental Management and Biodiversity Conservation Plan implemented by the IUCN Bangladesh Country Office, which involves a cooperative effort between the World Bank and Bangladesh Government to identify policy reforms, investments, and technical assistance needed to address environmental priorities and support the livelihoods of local communities. (14) While it recognizes the importance of spreading awareness of mangrove biodiversity and the significance of ecosystem services, this project too lacks specific regulations regarding shrimp aquaculture farming.

Clearly, more effective conservation strategies must be explored and enacted with regards to managing shrimp aquaculture systems, increasing government accountability and oversight of largescale shrimp projects, and integrating coastal communities into policymaking.

Policies should be focused on sustainable and sociallyintegrated shrimp aquaculture practices, recognizing a dual need to maintain high shrimp yields and preserve the livelihoods of coastal communities. Potential courses of action include stricter measurement and reduction of effluent discharge, sustainable revisions to aquaculture systems, intensified government oversight of farming practices, and implementation of Community-Based Fisheries Management (CBFM) in policy decisions.

Given the scope and value of the shrimp industry to coastal Asian economies, finding a policy solution targeted at the management of shrimp aquaculture and preservation of local livelihoods is critical to Sundarban conservation.

Also given the lack of real current political investment in Sundarban conservation, these policies should operate on both proximate and ultimate levels to minimize the immediate environmental and socioeconomic effects on coastal communities, increase government oversight over shrimp farms, and integrate traditional fisheries into shrimp aquaculture projects to maximize economic benefits for both interests. (15) Concerted efforts through CBFM may facilitate knowledge-sharing between interests historically at conflict and have come a long way in reversing common perceptions of mangroves as “smelly, unproductive wastelands” to the celebrated and respected “green lungs of Mother Earth”. (5) These policy recommendations will help the Sundarbans maintain their critical respiratory function.

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ENTERING THE ALLIUM:

A Lighter Side of Science

Illustrations by Leanne Gan

Real News: True Things That Happened New financial aid: Interdisciplinary research University partners with area team vows to address reallyfirms to offer post-graduation job as part of financial aid for loud-squeaky-shoes-inincoming computer science students.

Thompson-when-it-rains issue Proposed experiential Contentious campus solar learning course initiative completed draws concern, After nearly three years of review and discussion, administration’s scale model of intense interest campus now fully powered by sustainable solar Building off of popular courses such as “The Idea of Wine”, new immersive connections course CONN465: Fermentation, Imbibement, and Impairment pushes the boundaries of experiential learning and human decency.

Physics student reportedly “pretty sure the cat is dead”

energy.

Sophomore pre-med student assures roommate over health concerns: “Trust me, I’m definitely going to be a doctor one day. We just learned about this in cell bio.

You’re totally fine.”

Opening crew at Oppenheimer Café Forgets to Unlock Door Dazed and incoherent students gathered outside, demanding answers and devolving into a rather lackluster melee: “I really think the lack of coffee had them struggling to form a respectable angry mob” stated an observer.

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COSMopolitan d r e n Exploring your

G-holed torus: the do’s and definititely don’ts

Duncan Bennett: An exclusive interview with this highly logical bachelor

∞

tips to spice up any function

how pure is your math?

Take the Quiz!

UNIVERSITY OF PUGET SOUND | 41

A Student’s Guide to

[Astronomy[

Astronomers 4/18/16 4:12 AM

Comment: Astrology

BY MEGAN REICH

Bos taurus (m) April 20- May 20 The theme of this semester for you is celebration of change. Adventures await you, and your inner belief system will be shaken - prepare to experience some religious or philosophical upheaval.

You may find yourself taking extra classes or challenging yourself academically. Consider applying for teaching or tutoring opportunities! Don’t waste your precious energy - put in the hard work now to get results later.

Dizygotic offspring May 21 - June 20 You will be tested in multiple areas of your life this semester. You might find yourself feeling burnt out, or realizing you don’t have as much motivation as you have had in the past.

But this won’t shake your confidence! This streak of determinism will be accompanied by a surge of good luck around midterms. This year will also be a prime time for developing close relationships with your professors. Respect your inner curiosity and connect with them - visit their office hours frequently.

Infraorder Brachyura June 21 - July 22 Compared to last year, this semester will pose new barriers and difficulties for you, but it will also mark a time for pursuing creative or artistic pursuits.

Take the time to transform your abstract ideas into something tangible - engage in research opportunities and presenting your findings to both the scholarly community and general public. However, you may also find yourself feeling emotionally sensitive. You are currently prone to poor decision-making skills - be careful. Expand your horizons but don’t spread yourself too thin.

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Panthera leo July 23 - August 22 This semester marks a time of harmonious relationships in home and family life. You will discover new strong passions related to a class you were originally reluctant to take - pay no heed to your previous expectation - find what you love and delve yourself into the joy of learning. Look for opportunities to widen your perspective. This is a good time for traveling or studying abroad, and with this you may find yourself taking on a greater set of responsibilities.

Prereproductive individual August 23 - September 22 You may come face to face with some unpleasant truths this semester, and your ego will take a beating.

A buildup of tense energy over second thoughts regarding your career aspirations will lead to feelings of frustration. Try your best to release this held-up negativity through coping activities like exercise.

Soon, however, will be a prime time to reconsider your goals and set a more optimistic outlook on the months ahead. Do not become disheartened by bumps in the road!

Le Châtelier’s Muse September 23 - October 22 This semester marks a time of great material and spiritual growth. You will feel emotionally defensive in the face of critical judgement from your peers and professors, but try not to take their comments seriously. Additionally, you will be triggered into positive actions of compassion and bravery, and karma will deservedly reward you for your efforts. The latter half of this calendar cycle will be challenging and draining for you, with struggles to reconcile relationship tensions. Schedule more important projects in the first half of the year to prevent total burnout later on.

Order Scorpiones October 23 - November 21 While you will encounter no major misfortunes this semester, there will also be a lack of any major streaks of luck. In order to gain more fulfillment in life, consider joining social groups or clubs related to your academic interests. Your observations of the world around you will be more astute than ever. Promotion or recognition for your efforts may be in order.

Additionally, setting new goals will be an important process for you, and negative consequences may result from lack of planning Homo sapiens x Equus ferus November 22 - December 21 You may have been feeling your confidence lagging in classes lately. To combat this, try to avoid overidealizing certain people or concepts, as you may be particularly vulnerable to deception or manipulation.

This semester marks a theme of healing: focus on helping others.Collaborations and group projects may actually be important occasions for personal growth. You may encounter some initial resistance and will have to work hard to justify your intentions and plans, but it will be worth it!

Capra spp.

December 22 - January 19 In troubling times, look for outside support from fellow students and professors. Do not isolate yourself - these people will be more friendly than you expect!

There may be some serious change or unsettling events, but the worst will pass shortly. Financial success is in store for you after this semester - plan ahead to ensure a positive internship or job, lest it go to waste. Also, try to prevent optimism from turning into greed. There may be a danger of acting impulsively.

Hydrophile January 20 - February 18 This semester will be an exciting one for you, but most of the action will occur in the latter half of the year. You may experience a major personality shift, now is the time to come out of your shell and take some social risks. You will experience a very hectic week with the onset of finals. Be careful with a lack of clarity and general scatteredness during this time, and focus on steady progress towards your long term goals. This year marks a solid time to fulfill vital obligations or duties.

Gill-bearing craniates lacking digital limbs February 19 - March 20 This next semester could be a turning point for you academically. WIth two eclipses in your own sign, this is the time to redefine your priorities. Health will be on your radar - make self-care a priority. Try not to internalize any aggression that arises in the work that you do. Experiment with meditation! If you get stuck in solving a problem, take a step away from it for a few days. Open communication will be key.

Subfamily Caprinae (m) March 21 - April 19 This next semester will be a period of great personal growth for you. Challenging, thought-provoking courses may bring about a significant expansion of philosophy and spirituality. Maintain an accepting attitude to obstacles that may come your way. With Jupiter in the house of the workplace, this marks a prime time for job-hunting, especially for senior students. Take advantage of your sense of drive!

UNIVERSITY OF PUGET SOUND | 43

CITATIONS carbon nanotubes 1. Adams, Thomas A. ”Equilibrium Structure” Michigan State University, http://www.pa.msu.edu/cmp/csc/ntproperties/equilibriumstructure.html.

Accessed November 26 2015.

2. Echternach, Juliana, Dhall, Rohan, and Cronin, Steve. “Growth on pnjunction devices and Chip-to-Chip Transfers.” Thompson Presentation, University of Southern California.

3. “Carbon Nanotube Applications and Uses.” UnderstandingNano.com. http://www.understandingnano.com/nanotubes-carbon.html. Accessed November 26 2015.

4. Echternach, Juliana, Dhall, Rohan, Chen, Jihan, and Cronin, Steve.

“Suspended Carbon Nanotube Growth on pn-junction devices and Chipto-Chip Transfers.” Research Poster. University of Southern California.

CRISPR Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010).

Mali, P. et al. RNA-Guided Human Genome Engineering via Cas9. Science 339, 823–826 (2013).

Cong, L. et al. Multiplex Genome Engineering Using CRISPR/Cas Systems.

Science 339, 819–823 (2013).

Colombo Colombo, Lisa and Luc Boisvert. “Synthesis of Ligands and Iron Precursors to Form Iron-Based Hydrogenation Catalysts.” Department of Chemistry, University of Puget Sound, Tacoma, WA. Briana Greenwood Greenwood, Brianna L., “Pruning the Garden of the Nervous System: Neurodegeneration in Drosophila” (2015). Summer Research. Paper 244. http://soundideas.pugetsound.edu/summer_research/244 John Evans Evans, John, “Oncogene Characterization and Mapping” (2015). Summer Research. Paper 241. http://soundideas.pugetsound.edu/summer_research/241 Borneo (1) Sodhi, N.S., L.P. Koh, B.W. Brook, and P.K.L. Ng. 2004. Southeast Asian biodiversity: an impending disaster. TRENDS in Ecology and Evolution. 19:654-660.

(2) Rosen, G.E. and K.F. Smith. 2010. Summarizing the evidence on the international trade in illegal wildlife. EcoHealth. 7:24-32.

(3) Meijaard, E., D. Sheil, R. Nasi, D. Augeri, B. Rosenbaum, D. Iskandar, T. Setyawati, M. Lammertink, I. Rachmatika, A. Wong, T. Soehartono, S. Stanley and T. O’Brien. 2005. Life after logging: Reconciling wildlife conservation and production forestry in Indonesian Borneo. CIFOR and UNESCO. pp 370.

(4) TRAFFIC, 2008. “What’s Driving the Wildlife Trade? A Review of Expert Opinion on Economic and Social Drivers of the Wildlife Trade and Trade Control Efforts in Cambodia, Indonesia, Lao PDR and Vietnam”. East Asia and Pacific Region Sustainable Development Discussion Papers. East Asia and Pacific Region Sustainable Development Department, World Bank, Washington, DC. pp 120.

(5) The World Bank, 2005. “Going, Going, Gone…The Illegal Trade in Wildlife in East and Southeast Asia”. Environment and Social Development East Asia and Pacific Region Development Paper. East Asia and Pacific Region of the World Bank,

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Washington, DC. pp 32.

Mangroves Sources Cited: (1) Gopel, B. and M. Chauhan. 2006. “Biodiversity and its conservation in the Sundarban Mangrove Ecosystem.” Aquatic Science 68: 338-354.

(2) Biswas, H., S.K. Mukhopadhyay, and T.K. De. 2004. “Biogenic control on the air-water carbon dioxide exchange in the Sundarban mangrove environment, northeast coast of Bay of Bengal, India.” Limnology and Oceanography 49: 95-101.

(3) Ganguly, D., R. Ray, C. Chowdhury, M. Dey, S. Das, M.K. Dutta, S.K. Mandal, N. Majumder, T.K. De, S.K. Mukopadhyay, and T.K. Jana.

2011. “Carbon sequestration and annual increase of carbon stock in a mangrove forest.” Atmospheric Environment. Accessed December 3, 2015.

DOI:10.1016/j.atmosenv.2011.04.074.

(4) Walters, B.B., P. Ronnback, J.M. Kovacs, B. Crona, S.A. Hussain, R. Badola, J.H. Primavera, E. Barbier, and F. Dahdouh-Guebes. 2007.

“Ethnobiology, socio-economics and management of mangrove forests: a review.” Aquatic Botany 89: 220-236.

(5) Hoq, M.E. 2007. “An analysis of fisheries exploitation and management practices in Sundarbans mangrove ecosystem, Bangladesh.” Ocean and Coastal Management 50: 411-427.

(6) Paez-osuna, F. 2001. “The Environmental Impact of Shrimp Aquaculture: Causes, Effects, and Mitigating Alternatives.” Environmental Management 28: 131-140.

(7) Hein, L. 2000. “Impact of shrimp farming on mangroves along India’s East Coast.” Unasylva 51: 48-55.

(8) Islam, M.S. and M. Haque. 2004. “The mangrove-based coastal and nearshore fisheries of Bangladesh: ecology, exploitation, and management.” Reviews in Fish Biology and Fisheries 14: 153-180.

(9) Rahman, Mohammed M., M. Motuir Rahman, and K.S. Islam. 2010.

“The causes of deterioration of Sundarban mangrove forest ecosystem of Bangladesh: conservation and sustainable management issues.”

International Journal of the AACL Bioflux Society 3: 1-14.

(10) Environmental Justice Foundation. 2004. “Farming the Sea, Costing the Earth.” Environmental Justice Reports. 1-81. Accessed December 4, 2015. http://www.ejfoundation.org/reports.

(12) Flegel, T.W. and V. Alday-Sanz. 1998. “The crisis in Asian shrimp aquaculture: current status and future needs.” Journal of Applied Ichthyology 14: 269-273.

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